[1] "ofn"            "-oTCOADREAD-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/COADREAD-TP/19775152/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/19781252/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=615, common to both=612
[1]  82 612
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               562 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               562 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              117               495 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              117               495 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               490 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              122               490 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              120               492 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              120               492 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               540 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               540 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               98               514 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               98               514 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               592 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               592 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               591 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               591 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               509 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               509 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               548 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               548 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              124               488 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              124               488 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               501 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               501 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              348               264 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              348               264 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              310               302 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              310               302 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              170               442 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              170               442 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              314               298 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              314               298 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              122               490 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              122               490 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               511 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               511 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                563 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                563 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                583 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                583 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                85                527 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                85                527 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                77                535 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                77                535 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                485 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                485 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                501 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                501 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               367                245 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               367                245 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                569 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                569 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                597 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                597 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               147                465 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               147                465 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               145                467 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               145                467 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                574 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                574 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               110                502 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               110                502 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                579 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                579 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                593 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                593 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               104                508 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               104                508 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               114                498 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               114                498 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               350                262 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               350                262 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               462                150 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               462                150 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                578 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                578 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                589 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                589 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               98               514 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               98               514 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              107               505 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              107               505 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              137               475 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              137               475 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               78               534 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               78               534 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               595 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               595 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               598 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               598 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               69               543 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               69               543 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               568 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               568 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              195               417 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              195               417 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              188               424 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              188               424 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               86               526 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               86               526 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              121               491 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              121               491 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               567 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               567 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               544 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               544 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               609 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               609 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               607 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               607 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              216               396 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              216               396 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               576 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               576 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               76               536 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               76               536 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               77               535 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               77               535 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                512 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                512 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                502 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                502 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                538 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                538 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                520 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                520 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                542 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                542 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                70                542 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                70                542 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                592 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                592 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               204                408 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               204                408 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               228                384 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               228                384 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                41                571 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                41                571 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                569 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                569 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               338                274 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               338                274 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                96                516 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                96                516 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               377                235 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               377                235 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               407                205 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               407                205 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                549 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                549 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                557 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                557 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                67                545 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                67                545 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                606 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                606 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               192                420 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               192                420 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               201                411 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               201                411 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               90               522 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               90               522 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               534 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               534 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 612 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=105,	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=358,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 612 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "TUMOR_TISSUE_SITE"     "PATHOLOGIC_STAGE"     
 [4] "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"    
 [7] "GENDER"                "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"    
[10] "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES" "RACE"                 
[13] "ETHNICITY"            
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 20 106 417  67 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 106 417  67 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 106 417  67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 106 417  67 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
345 150 115 
[1] "table(vv)"
vv
 N0  N1  N2 
345 150 115 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
345 150 115 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
345 150 115 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, 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    36  13
  1P GAIN WILD-TYPE 436 108
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               544 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               108 
$`1P GAIN MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-6654 
       39.45        43.76        44.91        45.60        16.57        23.87 
TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3855 
       13.02        54.02         2.01        15.02        19.00        32.05 
TCGA-AA-3973 TCGA-AA-A01D TCGA-AA-A02E TCGA-AD-6888 TCGA-AY-A69D TCGA-AZ-4682 
       13.05        10.98         2.96        15.52        17.85        22.36 
TCGA-AZ-4684 TCGA-CA-5255 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5864 
       65.00         3.06        12.20        49.08         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        2.96        14.99        15.12         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A28M TCGA-NH-A50T TCGA-QG-A5YV TCGA-RU-A8FL 
       14.30       119.70        95.18        18.18        42.77        30.28 
TCGA-AF-2692 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3611 
       13.55        14.50        32.02        46.03        34.03        13.94 
TCGA-AG-A026 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 
        1.94        15.02        24.13        10.78         8.45         9.96 
TCGA-G5-6641 
       26.43 

$`1P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       13.94        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.16        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.05         6.97        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
        1.41         5.65        32.94         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
        5.23        11.74         3.19         1.61        12.69         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58         3.68         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        74.79        79.69        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       70.03        24.13        39.48        17.23        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        19.99        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.97        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        11.51        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       12.46        18.28        55.76        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.48              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           119.70            148.01 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           15.120            20.155 
[1] "1.5 - 119.7 (15.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    37  11
  1P GAIN WILD-TYPE 409 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37   11
  1P GAIN WILD-TYPE  409  151
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON               37               409
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P GAIN MUTATED         7        0        2        13         1         0
  1P GAIN WILD-TYPE      97        1       34       160         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          3          4          7        6
  1P GAIN WILD-TYPE        25         15         79         47       57
                   vv
clus                STAGE IVA STAGE IVB
  1P GAIN MUTATED           6         0
  1P GAIN WILD-TYPE        20         2
D1V4, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  7                97
  STAGE IA                 0                 1
  STAGE II                 2                34
  STAGE IIA               13               160
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               3                15
  STAGE IIIB               4                79
  STAGE IIIC               7                47
  STAGE IV                 6                57
  STAGE IVA                6                20
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     2   6  34   8
  1P GAIN WILD-TYPE  18 100 383  59
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               2                18
  T2               6               100
  T3              34               383
  T4               8                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
  1P GAIN MUTATED    25  12  13
  1P GAIN WILD-TYPE 320 138 102
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              25               320
  N1              12               138
  N2              13               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    31  10
  1P GAIN WILD-TYPE 419  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     31   10
  1P GAIN WILD-TYPE  419   78
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              31               419
  1              10                78
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    20  30
  1P GAIN WILD-TYPE 267 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20   30
  1P GAIN WILD-TYPE  267  295
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              20               267
  MALE                30               295
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    38   3
  1P GAIN WILD-TYPE 408  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     38    3
  1P GAIN WILD-TYPE  408   25
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               38               408
  YES               3                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                     35                             2
  1P GAIN WILD-TYPE                  347                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                       8                              3
  1P GAIN WILD-TYPE                   138                             10
D1V10, multiclass
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        35               347
  COLON MUCINOUS ADENOCARCINOMA                2                58
  RECTAL ADENOCARCINOMA                        8               138
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    36   1   4   4
  1P GAIN WILD-TYPE 406   4  33  25
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              36               406
  R1               1                 4
  R2               4                33
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     2
  1P GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           6    28
  1P GAIN WILD-TYPE                        58   264
D1V13, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      6                58
  WHITE                                         28               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  35
  1P GAIN WILD-TYPE   4 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   35
  1P GAIN WILD-TYPE    4  313
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              35               313
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    86  28
  1Q GAIN WILD-TYPE 386  93
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              114               479 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               28                93 
$`1Q GAIN MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       39.45        43.76        43.76        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       16.57        36.53        32.45        24.16        24.69        23.87 
TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
        5.03        13.02        13.94        78.08        54.02         2.01 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3855 
       47.05        15.02        19.00         5.03        10.06        32.05 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3973 
       31.07        17.03        27.02        12.99        33.01        13.05 
TCGA-AA-3994 TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y 
       27.02        10.98        35.01        26.01         2.96        39.98 
TCGA-AD-6888 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
       15.52        14.50        17.85        22.36        65.00        12.10 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 
       11.74         3.06        12.20        49.08        37.02        25.02 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 
       22.98        15.02         5.03        15.02         2.96        14.99 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        1.32        15.12        17.85         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28M 
       14.30       119.70        92.75        81.37        35.97        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 
        8.61        31.96        11.11        47.41        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL 
       65.85        39.42        18.18         9.93        42.77        30.28 
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 
       13.55        14.50        15.39        10.39        32.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3999 
       34.03        34.03         6.05        13.94        19.04        28.04 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 
       36.03        31.00        70.03        51.98         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-6155 
       38.56         0.69         0.72         9.37        11.01        13.97 
TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 
       15.02       129.27        24.13        20.55         8.61        10.78 
TCGA-EI-6885 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6641 
       13.64         8.45         9.96         0.69         0.76        26.43 

$`1Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 
       43.43        42.90        24.33        42.28        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        34.65        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        20.61        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 
       19.99        19.99        61.02         6.05         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       25.02        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        5.79        22.42        27.42        10.88         0.20        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23         3.19         1.61        12.69         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.03        30.08        32.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58         3.68         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        26.47       119.93        60.79       117.07        98.24 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
      133.18        28.21         8.35        23.51        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        85.48        63.62        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U 
       26.17        91.79        46.75        74.79        79.69        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33        15.65        12.79        17.85        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       70.03        24.13        39.48        17.23        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       34.49        37.74        10.39        16.83        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03         8.98        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       57.24        51.48        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       16.31        16.41        11.51        17.46        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       31.30        28.57         0.39        32.19         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12        12.46        18.28        55.76        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.69              0.00 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            148.01 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            19.02             19.99 
[1] "0.7 - 129.3 (19.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    81  34
  1Q GAIN WILD-TYPE 365 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     81   34
  1Q GAIN WILD-TYPE  365  128
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON               81               365
  RECTUM              34               128
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q GAIN MUTATED        14        0        7        27         2         0
  1Q GAIN WILD-TYPE      90        1       29       146         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           4          4         15         15       19
  1Q GAIN WILD-TYPE        22         14         68         39       44
                   vv
clus                STAGE IVA STAGE IVB
  1Q GAIN MUTATED           8         0
  1Q GAIN WILD-TYPE        18         2
D2V4, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 7                29
  STAGE IIA               27               146
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                4                22
  STAGE IIIA               4                14
  STAGE IIIB              15                68
  STAGE IIIC              15                39
  STAGE IV                19                44
  STAGE IVA                8                18
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED     4  14  78  21
  1Q GAIN WILD-TYPE  16  92 339  46
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               4                16
  T2              14                92
  T3              78               339
  T4              21                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    55  30  31
  1Q GAIN WILD-TYPE 290 120  84
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              55               290
  N1              30               120
  N2              31                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    78  25
  1Q GAIN WILD-TYPE 372  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     78   25
  1Q GAIN WILD-TYPE  372   63
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              78               372
  1              25                63
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    50  67
  1Q GAIN WILD-TYPE 237 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     50   67
  1Q GAIN WILD-TYPE  237  258
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              50               237
  MALE                67               258
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    84   9
  1Q GAIN WILD-TYPE 362  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     84    9
  1Q GAIN WILD-TYPE  362   19
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               84               362
  YES               9                19
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                     75                             6
  1Q GAIN WILD-TYPE                  307                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                      29                              4
  1Q GAIN WILD-TYPE                   117                              9
D2V10, multiclass
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        75               307
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       29               117
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    82   1  10   5
  1Q GAIN WILD-TYPE 360   4  27  24
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              82               360
  R1               1                 4
  R2              10                27
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     2
  1Q GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          11    64
  1Q GAIN WILD-TYPE                        53   228
D2V13, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     11                53
  WHITE                                         64               228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  73
  1Q GAIN WILD-TYPE   4 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   73
  1Q GAIN WILD-TYPE    4  275
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              73               275
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    89  27
  2P GAIN WILD-TYPE 383  94
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               477 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               27                94 
$`2P GAIN MUTATED`
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3807 
       15.62         1.61        39.45        43.76        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 
       36.53        14.53        30.44        32.71        29.16        24.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3532 
       24.69        23.87         1.02         9.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 
       29.00        19.99        50.04        15.02        37.05        10.06 
TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-A00L TCGA-AA-A01I 
       35.05        33.07        24.03        16.08        38.04        31.00 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 
        1.02        26.01        21.37        15.52         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 
       27.42        16.44        16.31        18.84         5.13         3.19 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 
        0.07        12.20        10.06        85.45         9.99         8.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        17.03        15.02         2.96        29.03 
TCGA-CM-6166 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 
       21.99        45.40        55.92         4.80        17.13        14.30 
TCGA-D5-6929 TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 
        4.80         7.50         7.76        35.97         8.61         8.35 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A6GC 
       74.56        63.62        74.79        79.69        18.18        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       17.85        29.46        32.98        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 
       17.23        16.83        86.63        65.98        36.03        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 
       34.03        34.03        19.99        19.99         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 
       46.03        12.00        31.00        70.03        38.04        26.43 
TCGA-BM-6198 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 
       10.19        78.12         7.17        21.01         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       15.02        27.95         4.01       129.27        51.48        20.55 
TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6233 
       16.31        13.64         9.96        49.51        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

$`2P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       13.94        16.57        37.05        37.25        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 
        7.04         3.02         1.02        37.05        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       19.07        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        19.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       14.93         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 
        3.06         2.14         3.25         3.29        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        70.16        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       37.02        25.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       12.00        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        82.39        23.51        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        85.48        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        91.79        46.75        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        9.93        15.65        16.80        42.77         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       21.90        11.90        70.03        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        11.84        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        3.98        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07         1.02        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       41.00        38.56         1.45         0.69         0.72         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        13.97        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       11.51        10.78        17.46        11.97         8.45        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6641 
        1.12         0.76        26.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            148.01 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            21.68             19.96 
[1] "0.1 - 129.3 (21.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    81  41
  2P GAIN WILD-TYPE 365 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     81   41
  2P GAIN WILD-TYPE  365  121
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON               81               365
  RECTUM              41               121
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P GAIN MUTATED        16        0        8        30         0         2
  2P GAIN WILD-TYPE      88        1       28       143        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          2         21         14       12
  2P GAIN WILD-TYPE        20         16         62         40       51
                   vv
clus                STAGE IVA STAGE IVB
  2P GAIN MUTATED           7         1
  2P GAIN WILD-TYPE        19         1
D3V4, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 8                28
  STAGE IIA               30               143
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                6                20
  STAGE IIIA               2                16
  STAGE IIIB              21                62
  STAGE IIIC              14                40
  STAGE IV                12                51
  STAGE IVA                7                19
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED     2  18  91  10
  2P GAIN WILD-TYPE  18  88 326  57
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               2                18
  T2              18                88
  T3              91               326
  T4              10                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2P GAIN MUTATED    59  30  32
  2P GAIN WILD-TYPE 286 120  83
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              59               286
  N1              30               120
  N2              32                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    81  20
  2P GAIN WILD-TYPE 369  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     81   20
  2P GAIN WILD-TYPE  369   68
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              81               369
  1              20                68
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    61  61
  2P GAIN WILD-TYPE 226 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     61   61
  2P GAIN WILD-TYPE  226  264
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              61               226
  MALE                61               264
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    89   9
  2P GAIN WILD-TYPE 357  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     89    9
  2P GAIN WILD-TYPE  357   19
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               89               357
  YES               9                19
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                     75                             6
  2P GAIN WILD-TYPE                  307                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                      41                              0
  2P GAIN WILD-TYPE                   105                             13
D3V10, multiclass
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        75               307
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       41               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    86   3   5  10
  2P GAIN WILD-TYPE 356   2  32  19
D3V11, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              86               356
  R1               3                 2
  R2               5                32
  RX              10                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     3
  2P GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          18    67
  2P GAIN WILD-TYPE                        46   225
D3V13, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 9
  BLACK OR AFRICAN AMERICAN                     18                46
  WHITE                                         67               225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  82
  2P GAIN WILD-TYPE   3 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   82
  2P GAIN WILD-TYPE    3  266
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              82               266
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    88  27
  2Q GAIN WILD-TYPE 384  94
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              115               478 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               27                94 
$`2Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 
       15.62         1.61        39.45        43.76        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 
       14.53        30.44        32.71        29.16        24.16        24.69 
TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       23.87         1.02         9.07        34.03        29.00        29.00 
TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       19.99        50.04        15.02        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S 
       35.05        33.07        24.03        16.08        31.00         1.02 
TCGA-AA-A01X TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       26.01        21.37        15.52         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6716 
       16.44        16.31        18.84         5.13         3.19        12.20 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6161 
       85.45         9.99         8.02        29.06         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 
        2.96        29.03        21.99        14.99        45.40        55.92 
TCGA-D5-6537 TCGA-D5-6538 TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F 
        4.80        17.13         7.50         7.76        14.04        35.97 
TCGA-F4-6459 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 
        8.61         8.35        74.56        63.62        39.42        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX 
       79.69        18.18        12.79        17.85        29.46        32.98 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 
       30.28        24.13        39.48        17.23        10.39        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3591 
       15.39        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4007 
       34.03        19.99        19.99         1.02        48.03         1.02 
TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 
       46.03        12.00        31.00        70.03        38.04        26.43 
TCGA-BM-6198 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.19        78.12         7.17         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 
       27.95         4.01       129.27         2.40        20.55        16.31 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       13.64         9.96        49.51         0.76        12.46        18.28 
TCGA-G5-6572 
       47.08 

$`2Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       13.94        16.57        37.05        37.25        37.02        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.06        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        21.76        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
        0.00        19.07        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        11.01         5.98        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        19.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       14.93         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        0.07        56.55         0.79         0.72        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       75.95        58.39         1.41         5.65        32.94       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 
       12.76        10.06        14.30        17.56       148.01        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.26        19.59        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       18.25         1.32        43.27        15.12        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       44.32       131.51       135.65       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        47.41        35.31       133.18        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       42.77         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        37.74        14.50 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        11.84        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        3.98        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07         1.02        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       41.00        38.56         1.45         0.69         0.72         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       21.01        11.01        15.02        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12        55.76        26.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.76              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            148.01 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            20.55             19.99 
[1] "0.8 - 129.3 (20.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    77  43
  2Q GAIN WILD-TYPE 369 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     77   43
  2Q GAIN WILD-TYPE  369  119
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON               77               369
  RECTUM              43               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q GAIN MUTATED        16        0        8        28         0         2
  2Q GAIN WILD-TYPE      88        1       28       145        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           7          2         20         15       13
  2Q GAIN WILD-TYPE        19         16         63         39       50
                   vv
clus                STAGE IVA STAGE IVB
  2Q GAIN MUTATED           5         1
  2Q GAIN WILD-TYPE        21         1
D4V4, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 8                28
  STAGE IIA               28               145
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                7                19
  STAGE IIIA               2                16
  STAGE IIIB              20                63
  STAGE IIIC              15                39
  STAGE IV                13                50
  STAGE IVA                5                21
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED     2  18  89  10
  2Q GAIN WILD-TYPE  18  88 328  57
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                18
  T2              18                88
  T3              89               328
  T4              10                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2Q GAIN MUTATED    57  29  33
  2Q GAIN WILD-TYPE 288 121  82
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              57               288
  N1              29               121
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    80  19
  2Q GAIN WILD-TYPE 370  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     80   19
  2Q GAIN WILD-TYPE  370   69
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              80               370
  1              19                69
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    61  59
  2Q GAIN WILD-TYPE 226 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     61   59
  2Q GAIN WILD-TYPE  226  266
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              61               226
  MALE                59               266
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    87  10
  2Q GAIN WILD-TYPE 359  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     87   10
  2Q GAIN WILD-TYPE  359   18
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               87               359
  YES              10                18
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                     71                             6
  2Q GAIN WILD-TYPE                  311                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                      43                              0
  2Q GAIN WILD-TYPE                   103                             13
D4V10, multiclass
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        71               311
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       43               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    85   2   6   8
  2Q GAIN WILD-TYPE 357   3  31  21
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              85               357
  R1               2                 3
  R2               6                31
  RX               8                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          20    64
  2Q GAIN WILD-TYPE                        44   228
D4V13, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     20                44
  WHITE                                         64               228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  79
  2Q GAIN WILD-TYPE   3 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   79
  2Q GAIN WILD-TYPE    3  269
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              79               269
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    58  12
  3P GAIN WILD-TYPE 414 109
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               70               523 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               109 
$`3P GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6782 
       12.66        43.76        37.02        29.16        24.13        20.28 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3685 TCGA-AA-3842 
       19.99        19.99         2.01        14.01        37.05        37.02 
TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T 
       24.03        16.08        26.01        34.03         1.02        33.04 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-A69D 
       41.00         5.79        22.42         0.20         0.95        17.85 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 
       29.56         1.61        12.69        17.03        15.02        29.03 
TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A288 
       13.05        10.06        15.12        12.49        14.30        14.04 
TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC 
        1.55        65.85        35.93        13.78        46.75        12.79 
TCGA-QL-A97D TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       21.90        20.02        10.39        34.03        34.03        34.03 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3896 TCGA-AG-4001 
       13.94        19.99        20.98         7.99         1.02        36.03 
TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A020 TCGA-CI-6623 TCGA-DC-4745 
       14.04         9.07        12.00        10.98         9.37        21.01 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5831 
        5.03        15.02         5.95        41.36       129.27         2.40 
TCGA-EI-6510 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
       18.28        11.97        28.57        32.19 

$`3P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       43.76        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         3.19         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 
       32.02        15.02         5.03        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        30.28        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       32.02        19.99        28.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95        36.03         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        12.39        78.12         7.17        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        8.98        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51        31.30         0.39         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.2               0.0 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            148.01 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            17.44             20.19 
[1] "0.2 - 129.3 (17.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    44  27
  3P GAIN WILD-TYPE 402 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     44   27
  3P GAIN WILD-TYPE  402  135
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON               44               402
  RECTUM              27               135
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P GAIN MUTATED         9        1        2        18         1         0
  3P GAIN WILD-TYPE      95        0       34       155         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           5          5          6          6        9
  3P GAIN WILD-TYPE        21         13         77         48       54
                   vv
clus                STAGE IVA STAGE IVB
  3P GAIN MUTATED           5         2
  3P GAIN WILD-TYPE        21         0
D5V4, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  9                95
  STAGE IA                 1                 0
  STAGE II                 2                34
  STAGE IIA               18               155
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                5                21
  STAGE IIIA               5                13
  STAGE IIIB               6                77
  STAGE IIIC               6                48
  STAGE IV                 9                54
  STAGE IVA                5                21
  STAGE IVB                2                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED     2  13  48   8
  3P GAIN WILD-TYPE  18  93 369  59
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                18
  T2              13                93
  T3              48               369
  T4               8                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
  3P GAIN MUTATED    34  20  18
  3P GAIN WILD-TYPE 311 130  97
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              34               311
  N1              20               130
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    43  14
  3P GAIN WILD-TYPE 407  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     43   14
  3P GAIN WILD-TYPE  407   74
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              43               407
  1              14                74
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    38  34
  3P GAIN WILD-TYPE 249 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   34
  3P GAIN WILD-TYPE  249  291
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              38               249
  MALE                34               291
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    53   3
  3P GAIN WILD-TYPE 393  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     53    3
  3P GAIN WILD-TYPE  393   25
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               53               393
  YES               3                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                     39                             5
  3P GAIN WILD-TYPE                  343                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                      26                              1
  3P GAIN WILD-TYPE                   120                             12
D5V10, multiclass
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        39               343
  COLON MUCINOUS ADENOCARCINOMA                5                55
  RECTAL ADENOCARCINOMA                       26               120
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    52   0   3   3
  3P GAIN WILD-TYPE 390   5  34  26
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              52               390
  R1               0                 5
  R2               3                34
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     1
  3P GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           7    36
  3P GAIN WILD-TYPE                        57   256
D5V13, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                      7                57
  WHITE                                         36               256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  41
  3P GAIN WILD-TYPE   5 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   41
  3P GAIN WILD-TYPE    5  307
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              41               307
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    76  19
  3Q GAIN WILD-TYPE 396 102
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               95               498 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               19               102 
$`3Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5667 
       12.66         1.61        43.76        37.02        36.53        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3532 
       27.09        25.08        20.61        21.76        20.28        29.00 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       13.02        19.99        19.99        78.08         2.01        14.01 
TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3976 
       37.05        37.02        17.03        24.03        16.08        26.01 
TCGA-AA-3979 TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6888 
       24.00        34.03         1.02        33.04        41.00        15.52 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A69D 
        5.79        22.42         0.20        14.50         0.95        17.85 
TCGA-AZ-4614 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-4750 TCGA-CM-5868 
        5.65        29.56         1.61        12.69         8.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 
       15.02         2.96        29.03        13.05        10.06        15.12 
TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A285 TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6294 
       12.49        14.30         6.12        14.04         1.55        28.21 
TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC 
       65.85        39.42        35.93        13.78        46.75        12.79 
TCGA-QL-A97D TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3591 
       21.90        37.74        10.39        20.02        10.39        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       34.03        34.03        13.94        19.99        20.98         7.99 
TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L 
       17.95         1.02        36.03        14.04         9.07        12.00 
TCGA-AG-A020 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 
       10.98         9.37        78.12        21.01         5.03        15.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 
        5.95         4.01        41.36         2.40        18.28        16.31 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       11.97        28.57         0.39        32.19         0.76 

$`3Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       15.62         4.80         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.43        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02         6.05         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
        5.03        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
        8.35        82.39        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        30.28        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       34.49        14.50        16.83        15.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        12.39         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02         8.98        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       19.99         5.03         5.29       126.44        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        49.51        31.30         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12        12.46        18.28        55.76        47.08        26.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.2               0.0 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.12            148.01 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            17.03             20.73 
[1] "0.2 - 78.1 (17.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.3"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    63  34
  3Q GAIN WILD-TYPE 383 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63   34
  3Q GAIN WILD-TYPE  383  128
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON               63               383
  RECTUM              34               128
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q GAIN MUTATED        11        1        4        24         1         0
  3Q GAIN WILD-TYPE      93        0       32       149         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           6          6         11          9       13
  3Q GAIN WILD-TYPE        20         12         72         45       50
                   vv
clus                STAGE IVA STAGE IVB
  3Q GAIN MUTATED           7         2
  3Q GAIN WILD-TYPE        19         0
D6V4, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 1                 0
  STAGE II                 4                32
  STAGE IIA               24               149
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               6                12
  STAGE IIIB              11                72
  STAGE IIIC               9                45
  STAGE IV                13                50
  STAGE IVA                7                19
  STAGE IVB                2                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED     4  14  69  10
  3Q GAIN WILD-TYPE  16  92 348  57
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               4                16
  T2              14                92
  T3              69               348
  T4              10                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3Q GAIN MUTATED    45  31  22
  3Q GAIN WILD-TYPE 300 119  93
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              45               300
  N1              31               119
  N2              22                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    59  20
  3Q GAIN WILD-TYPE 391  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     59   20
  3Q GAIN WILD-TYPE  391   68
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              59               391
  1              20                68
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    50  48
  3Q GAIN WILD-TYPE 237 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     50   48
  3Q GAIN WILD-TYPE  237  277
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              50               237
  MALE                48               277
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    73   5
  3Q GAIN WILD-TYPE 373  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     73    5
  3Q GAIN WILD-TYPE  373   23
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               73               373
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                     57                             6
  3Q GAIN WILD-TYPE                  325                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                      33                              1
  3Q GAIN WILD-TYPE                   113                             12
D6V10, multiclass
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        57               325
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       33               113
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    73   0   3   4
  3Q GAIN WILD-TYPE 369   5  34  25
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              73               369
  R1               0                 5
  R2               3                34
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1     1
  3Q GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          10    52
  3Q GAIN WILD-TYPE                        54   240
D6V13, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     10                54
  WHITE                                         52               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1  59
  3Q GAIN WILD-TYPE   4 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   59
  3Q GAIN WILD-TYPE    4  289
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              59               289
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    15   4
  4P GAIN WILD-TYPE 457 117
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               574 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               117 
$`4P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-A56B TCGA-AA-3560 TCGA-AA-3982 
       15.62        43.76        45.60        56.25        19.99        27.02 
TCGA-AD-A5EK TCGA-AY-A8YK TCGA-CM-5862 TCGA-G4-6307 TCGA-RU-A8FL TCGA-AG-3890 
       16.44        18.84         5.03        55.04        30.28        17.03 
TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A011 TCGA-DC-4749 TCGA-DC-6682 TCGA-DY-A1DG 
       32.02        46.03        37.02        11.01         4.01        51.48 
TCGA-EI-6510 
       18.28 

$`4P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       43.76        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        25.02        24.00        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       20.98        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             4.01              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            56.25            148.01 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            27.02             19.99 
[1] "4.0 - 56.2 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   9
  4P GAIN WILD-TYPE 435 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    9
  4P GAIN WILD-TYPE  435  153
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON               11               435
  RECTUM               9               153
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P GAIN MUTATED         4        0        1         4         0         0
  4P GAIN WILD-TYPE     100        1       35       169        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          0          4          1        1
  4P GAIN WILD-TYPE        25         18         79         53       62
                   vv
clus                STAGE IVA STAGE IVB
  4P GAIN MUTATED           4         0
  4P GAIN WILD-TYPE        22         2
D7V4, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  4               100
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA                4               169
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               0                18
  STAGE IIIB               4                79
  STAGE IIIC               1                53
  STAGE IV                 1                62
  STAGE IVA                4                22
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   5  15   0
  4P GAIN WILD-TYPE  20 101 402  67
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                20
  T2               5               101
  T3              15               402
  T4               0                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P GAIN MUTATED    10   6   4
  4P GAIN WILD-TYPE 335 144 111
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              10               335
  N1               6               144
  N2               4               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12   4
  4P GAIN WILD-TYPE 438  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12    4
  4P GAIN WILD-TYPE  438   84
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              12               438
  1               4                84
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  14
  4P GAIN WILD-TYPE 281 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   14
  4P GAIN WILD-TYPE  281  311
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               281
  MALE                14               311
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    16   1
  4P GAIN WILD-TYPE 430  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     16    1
  4P GAIN WILD-TYPE  430   27
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               16               430
  YES               1                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                     11                             0
  4P GAIN WILD-TYPE                  371                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                       9                              0
  4P GAIN WILD-TYPE                   137                             13
D7V10, multiclass
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        11               371
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    17   0   0   0
  4P GAIN WILD-TYPE 425   5  37  29
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              17               425
  R1               0                 5
  R2               0                37
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           5     9
  4P GAIN WILD-TYPE                        59   283
D7V13, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      5                59
  WHITE                                          9               283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  14
  4P GAIN WILD-TYPE   5 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   14
  4P GAIN WILD-TYPE    5  334
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              14               334
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    14   6
  4Q GAIN WILD-TYPE 458 115
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               573 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               115 
$`4Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-5659 TCGA-A6-A56B 
       43.76        24.33        45.60        37.02        30.44        56.25 
TCGA-AA-3560 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3982 TCGA-AD-A5EK TCGA-AY-A8YK 
       19.99        24.03        12.99        27.02        16.44        18.84 
TCGA-AZ-6607 TCGA-G4-6307 TCGA-RU-A8FL TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3902 
        3.19        55.04        30.28        17.03        35.01        32.02 
TCGA-DC-6682 TCGA-DY-A1DG 
        4.01        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30        21.90        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.19              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            56.25            148.01 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            28.65             19.99 
[1] "3.2 - 56.2 (28.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   5
  4Q GAIN WILD-TYPE 430 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    5
  4Q GAIN WILD-TYPE  430  157
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON               16               430
  RECTUM               5               157
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q GAIN MUTATED         3        0        0         5         0         0
  4Q GAIN WILD-TYPE     101        1       36       168        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          0          5          2        4
  4Q GAIN WILD-TYPE        26         18         78         52       59
                   vv
clus                STAGE IVA STAGE IVB
  4Q GAIN MUTATED           2         0
  4Q GAIN WILD-TYPE        24         2
D8V4, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  3               101
  STAGE IA                 0                 1
  STAGE II                 0                36
  STAGE IIA                5               168
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                0                26
  STAGE IIIA               0                18
  STAGE IIIB               5                78
  STAGE IIIC               2                52
  STAGE IV                 4                59
  STAGE IVA                2                24
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   3  16   2
  4Q GAIN WILD-TYPE  20 103 401  65
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                20
  T2               3               103
  T3              16               401
  T4               2                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4Q GAIN MUTATED     8   6   7
  4Q GAIN WILD-TYPE 337 144 108
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8               337
  N1               6               144
  N2               7               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    13   6
  4Q GAIN WILD-TYPE 437  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     13    6
  4Q GAIN WILD-TYPE  437   82
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              13               437
  1               6                82
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6  15
  4Q GAIN WILD-TYPE 281 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   15
  4Q GAIN WILD-TYPE  281  310
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               6               281
  MALE                15               310
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    18   0
  4Q GAIN WILD-TYPE 428  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18    0
  4Q GAIN WILD-TYPE  428   28
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               18               428
  YES               0                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                     16                             0
  4Q GAIN WILD-TYPE                  366                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                       5                              0
  4Q GAIN WILD-TYPE                   141                             13
D8V10, multiclass
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        16               366
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    16   0   2   0
  4Q GAIN WILD-TYPE 426   5  35  29
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              16               426
  R1               0                 5
  R2               2                35
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           4     9
  4Q GAIN WILD-TYPE                        60   283
D8V13, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      4                60
  WHITE                                          9               283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  13
  4Q GAIN WILD-TYPE   5 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   13
  4Q GAIN WILD-TYPE    5  335
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13               335
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    81  19
  5P GAIN WILD-TYPE 391 102
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              100               493 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19               102 
$`5P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       15.62        44.91        45.60        37.25        37.02        34.65 
TCGA-A6-4107 TCGA-A6-6650 TCGA-A6-6651 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 
       32.45        20.61        21.76        12.99        13.02        24.00 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3715 
       19.99         2.01        47.01         5.98        19.00        19.04 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3939 
       37.02        14.93         0.99        17.03        24.03        12.99 
TCGA-AA-3968 TCGA-AA-3976 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 
       21.99        26.01        51.98         2.96        40.96         5.79 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 
       16.44         0.92        18.84        49.41        29.56         1.61 
TCGA-CA-5254 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6167 
       12.69        25.02        13.02        32.02        15.02        14.99 
TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6929 
       13.02        11.01        19.59        17.75        14.30         4.80 
TCGA-D5-6931 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28K TCGA-DM-A28M 
       12.00        12.59         7.50         6.12        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6626 
       31.96         1.55        47.41        82.39        55.04        46.75 
TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-3911 TCGA-AF-6655 
       74.79        12.79         8.42        30.28        37.74        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 
       10.39        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-4001 TCGA-AG-4007 
       19.99         1.02        17.95        17.03        36.03         1.02 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G 
       25.97        36.03        12.00        31.00         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-5869 
       41.00        38.04         0.69         0.72        10.19         5.03 
TCGA-DC-6156 TCGA-DC-6683 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 
       15.02         5.03         2.40        16.31        11.51         9.96 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       28.57        32.19         0.53         0.76 

$`5P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3810 TCGA-A6-4105 
       35.11        13.94        16.57        37.05        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.05        15.02        11.01        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05        31.07        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
      106.75        22.36        65.00        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       12.10       100.01         5.23        11.74         3.19         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        1.91       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 
        2.96        29.03        16.04        21.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       35.31       133.18        28.21         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       67.30        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.85        16.80        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        8.02         7.07        20.05        24.00         1.02        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       15.95        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       19.99        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        15.95         9.07         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
       10.98        51.98        49.97        61.97        38.56         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         8.98        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45        49.51        31.30         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.53              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            98.24            148.01 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.92             20.19 
[1] "0.5 - 98.2 (18.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    67  36
  5P GAIN WILD-TYPE 379 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     67   36
  5P GAIN WILD-TYPE  379  126
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON               67               379
  RECTUM              36               126
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P GAIN MUTATED        12        0        4        26         1         1
  5P GAIN WILD-TYPE      92        1       32       147         9         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           3          5         13         16       13
  5P GAIN WILD-TYPE        23         13         70         38       50
                   vv
clus                STAGE IVA STAGE IVB
  5P GAIN MUTATED           5         1
  5P GAIN WILD-TYPE        21         1
D9V4, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 12                92
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               26               147
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                3                23
  STAGE IIIA               5                13
  STAGE IIIB              13                70
  STAGE IIIC              16                38
  STAGE IV                13                50
  STAGE IVA                5                21
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED     1  20  69  13
  5P GAIN WILD-TYPE  19  86 348  54
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                19
  T2              20                86
  T3              69               348
  T4              13                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P GAIN MUTATED    45  31  26
  5P GAIN WILD-TYPE 300 119  89
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               300
  N1              31               119
  N2              26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    70  18
  5P GAIN WILD-TYPE 380  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     70   18
  5P GAIN WILD-TYPE  380   70
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              70               380
  1              18                70
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    48  55
  5P GAIN WILD-TYPE 239 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     48   55
  5P GAIN WILD-TYPE  239  270
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              48               239
  MALE                55               270
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    68   9
  5P GAIN WILD-TYPE 378  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     68    9
  5P GAIN WILD-TYPE  378   19
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               68               378
  YES               9                19
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                     59                             8
  5P GAIN WILD-TYPE                  323                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                      36                              0
  5P GAIN WILD-TYPE                   110                             13
D9V10, multiclass
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        59               323
  COLON MUCINOUS ADENOCARCINOMA                8                52
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    76   1   9   2
  5P GAIN WILD-TYPE 366   4  28  27
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              76               366
  R1               1                 4
  R2               9                28
  RX               2                27
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     1
  5P GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          14    48
  5P GAIN WILD-TYPE                        50   244
D9V13, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     14                50
  WHITE                                         48               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0  60
  5P GAIN WILD-TYPE   5 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   60
  5P GAIN WILD-TYPE    5  288
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              60               288
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    51  12
  5Q GAIN WILD-TYPE 421 109
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               63               530 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               109 
$`5Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       15.62        44.91        45.60        37.25        34.65        32.45 
TCGA-A6-6650 TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 
       20.61         2.01         5.98        19.00        19.04        37.02 
TCGA-AA-3844 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3939 TCGA-AA-3976 TCGA-AA-A029 
       14.93         0.99        17.03        12.99        26.01        51.98 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6598 
        2.96        40.96         5.79        16.44        33.01        49.41 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6167 
       29.56        11.74        13.02        32.02        15.02        14.99 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-DM-A1D8 TCGA-DM-A28M TCGA-G4-6626 
       11.01        19.59        17.75        12.59        95.18        46.75 
TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       74.79        12.79         8.42        20.02        10.39        65.98 
TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 
       36.03        34.03        19.99         1.02        17.95        17.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02X TCGA-AG-A032 
        1.02        25.97        12.00        31.00        41.00        38.04 
TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6683 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
        0.69         0.72         5.03        16.31        11.51        11.97 
TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 
        9.96        32.19         0.53 

$`5Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 
       35.11        13.94        16.57        37.05        37.02        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       14.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 
       47.05        47.01        15.02        11.01        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05        31.07        31.07        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31         0.95        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.85        16.80        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        30.28        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N 
       10.39        14.50        16.83        15.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3887 
       32.98         0.99         0.99        19.04        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 
       19.99        28.04        36.03        14.04        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
       38.56         1.45        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        8.45        49.51        31.30        28.57         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.53              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            95.18            148.01 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           17.750            20.235 
[1] "0.5 - 95.2 (17.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    40  24
  5Q GAIN WILD-TYPE 406 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     40   24
  5Q GAIN WILD-TYPE  406  138
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON               40               406
  RECTUM              24               138
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q GAIN MUTATED         8        0        3        16         1         1
  5Q GAIN WILD-TYPE      96        1       33       157         9         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           2          4          6          8        9
  5Q GAIN WILD-TYPE        24         14         77         46       54
                   vv
clus                STAGE IVA STAGE IVB
  5Q GAIN MUTATED           2         1
  5Q GAIN WILD-TYPE        24         1
D10V4, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  8                96
  STAGE IA                 0                 1
  STAGE II                 3                33
  STAGE IIA               16               157
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               4                14
  STAGE IIIB               6                77
  STAGE IIIC               8                46
  STAGE IV                 9                54
  STAGE IVA                2                24
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED     0  14  42   8
  5Q GAIN WILD-TYPE  20  92 375  59
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                20
  T2              14                92
  T3              42               375
  T4               8                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
  5Q GAIN MUTATED    30  20  13
  5Q GAIN WILD-TYPE 315 130 102
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              30               315
  N1              20               130
  N2              13               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    44  11
  5Q GAIN WILD-TYPE 406  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     44   11
  5Q GAIN WILD-TYPE  406   77
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              44               406
  1              11                77
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    29  35
  5Q GAIN WILD-TYPE 258 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     29   35
  5Q GAIN WILD-TYPE  258  290
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              29               258
  MALE                35               290
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    44   6
  5Q GAIN WILD-TYPE 402  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     44    6
  5Q GAIN WILD-TYPE  402   22
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               44               402
  YES               6                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                     36                             4
  5Q GAIN WILD-TYPE                  346                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                      24                              0
  5Q GAIN WILD-TYPE                   122                             13
D10V10, multiclass
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        36               346
  COLON MUCINOUS ADENOCARCINOMA                4                56
  RECTAL ADENOCARCINOMA                       24               122
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    47   0   6   1
  5Q GAIN WILD-TYPE 395   5  31  28
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              47               395
  R1               0                 5
  R2               6                31
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          10    28
  5Q GAIN WILD-TYPE                        54   264
D10V13, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                     10                54
  WHITE                                         28               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  34
  5Q GAIN WILD-TYPE   5 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   34
  5Q GAIN WILD-TYPE    5  314
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              34               314
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    96  21
  6P GAIN WILD-TYPE 376 100
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              117               476 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               100 
$`6P GAIN MUTATED`
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       43.43        42.90        44.91        36.53        32.45        30.44 
TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-A56B TCGA-AA-3532 TCGA-AA-3534 
       29.19        25.08        20.61        56.25        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3685 
       12.99        13.02        24.00        19.99        15.02        37.05 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3869 
       85.05        10.06        35.05        37.02        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00F 
        2.01        20.98        21.99        27.02         7.96        34.03 
TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AU-3779 
       31.00        35.01         2.96        40.96        22.42        14.50 
TCGA-AY-4071 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 
        0.95        17.26        22.36        65.00        14.30        15.62 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 
        9.99         8.02        13.02        29.06        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5541 
        5.03        15.02        13.02        15.02        19.59        55.92 
TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        1.32        17.13        12.49         9.04         4.80        11.38 
TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
        7.50        14.04       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6311 
       31.96        35.74         1.55        82.39        63.62        39.42 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D 
       91.79        46.75        10.98        12.79        29.46        21.90 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       30.28        24.13        43.04        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       15.39        65.98        46.03        19.99        20.98        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
        1.02         1.02        14.04         1.02         3.98        46.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 
       36.03         9.07        12.00        31.00         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        6.05         9.37         5.03         8.98        15.02        27.95 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 
      129.27        20.55        15.85        17.69        49.51        28.57 
TCGA-F5-6810 TCGA-G5-6233 TCGA-G5-6641 
        0.39        18.28        26.43 

$`6P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        46.65        43.76        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        14.53        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       19.07        34.03        26.01         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        36.95        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        24.00        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.20        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.61        12.69         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 
       26.04        27.02        22.03        22.98        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       18.25        43.27        15.12        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       60.79        11.11        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       35.31       133.18        28.21         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        74.79        79.69        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 
       42.77        32.98         8.42        31.30        11.90        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       39.48        17.23        13.55        19.10        34.49        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        37.02        15.95         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       41.00        38.04        38.56         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.81        33.17         6.97         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
        7.17        21.01        11.01        15.02        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 
        2.40        19.96        20.91        17.00        18.28        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.39              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            148.01 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            20.98             19.99 
[1] "0.4 - 129.3 (21.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83  39
  6P GAIN WILD-TYPE 363 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83   39
  6P GAIN WILD-TYPE  363  123
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON               83               363
  RECTUM              39               123
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P GAIN MUTATED        18        0        3        24         2         1
  6P GAIN WILD-TYPE      86        1       33       149         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           5          6         22         16       15
  6P GAIN WILD-TYPE        21         12         61         38       48
                   vv
clus                STAGE IVA STAGE IVB
  6P GAIN MUTATED           9         1
  6P GAIN WILD-TYPE        17         1
D11V4, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 18                86
  STAGE IA                 0                 1
  STAGE II                 3                33
  STAGE IIA               24               149
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III                5                21
  STAGE IIIA               6                12
  STAGE IIIB              22                61
  STAGE IIIC              16                38
  STAGE IV                15                48
  STAGE IVA                9                17
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     6  18  86  14
  6P GAIN WILD-TYPE  14  88 331  53
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6                14
  T2              18                88
  T3              86               331
  T4              14                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6P GAIN MUTATED    54  31  38
  6P GAIN WILD-TYPE 291 119  77
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              54               291
  N1              31               119
  N2              38                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83  24
  6P GAIN WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83   24
  6P GAIN WILD-TYPE  367   64
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              83               367
  1              24                64
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    53  71
  6P GAIN WILD-TYPE 234 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     53   71
  6P GAIN WILD-TYPE  234  254
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              53               234
  MALE                71               254
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    84  10
  6P GAIN WILD-TYPE 362  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     84   10
  6P GAIN WILD-TYPE  362   18
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               84               362
  YES              10                18
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                     73                            10
  6P GAIN WILD-TYPE                  309                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                      38                              1
  6P GAIN WILD-TYPE                   108                             12
D11V10, multiclass
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        73               309
  COLON MUCINOUS ADENOCARCINOMA               10                50
  RECTAL ADENOCARCINOMA                       38               108
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    91   0  11   4
  6P GAIN WILD-TYPE 351   5  26  25
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              91               351
  R1               0                 5
  R2              11                26
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     1
  6P GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          15    63
  6P GAIN WILD-TYPE                        49   229
D11V13, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     15                49
  WHITE                                         63               229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0  75
  6P GAIN WILD-TYPE   5 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   75
  6P GAIN WILD-TYPE    5  273
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              75               273
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    87  18
  6Q GAIN WILD-TYPE 385 103
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              105               488 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               18               103 
$`6Q GAIN MUTATED`
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6142 
       43.43        42.90        44.91        30.44        29.19        25.08 
TCGA-A6-6650 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 
       20.61        29.00        29.00        26.01        12.99        24.00 
TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       19.99        15.02        37.05        85.05        10.06        35.05 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-A00F 
       37.02        17.03        27.02         2.01        20.98        34.03 
TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AU-3779 
       31.00        35.01         2.96        40.96        22.42        14.50 
TCGA-AY-4071 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 
        0.95        17.26         5.65        22.36        65.00        14.30 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
       15.62         9.99         8.02        13.02        29.06        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5541 
        5.03        15.02        13.02        15.02        19.59        55.92 
TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        1.32        17.13        12.49         9.04         4.80        11.38 
TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
        7.50        14.04       117.07        95.18         8.61        31.96 
TCGA-F4-6569 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6625 
       35.74        82.39        74.56        63.62        39.42        91.79 
TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       10.98        12.79        29.46        21.90        30.28        24.13 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3592 
       37.74        10.39        14.50        15.39        65.98        34.03 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 
       19.99        20.98        29.98         1.02         1.02         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
        3.98        46.03        36.03         9.07        12.00        31.00 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 
        0.72        10.19         6.05         9.37         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 
       15.02        27.95        51.48        20.55        15.85        17.69 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       49.51        28.57         0.39 

$`6Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        46.65        43.76        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
        8.05        19.07         0.00        19.07        34.03         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       50.04        47.05        47.01        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 
       36.00         5.03        26.99        19.04        19.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       17.03        24.03        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.20        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        75.95        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.03        22.98        30.08        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       18.25        43.27        15.12        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24        11.11        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       79.69        18.18        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        16.80        42.77        32.98         8.42        31.30 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       19.10        34.49        16.83        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        13.94         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       15.95         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.56         1.45         0.69        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        18.28        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        31.30        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.39              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           117.07            148.01 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            20.55             19.99 
[1] "0.4 - 117.1 (20.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    75  34
  6Q GAIN WILD-TYPE 371 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     75   34
  6Q GAIN WILD-TYPE  371  128
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON               75               371
  RECTUM              34               128
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q GAIN MUTATED        16        0        3        20         2         0
  6Q GAIN WILD-TYPE      88        1       33       153         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           5          5         19         14       13
  6Q GAIN WILD-TYPE        21         13         64         40       50
                   vv
clus                STAGE IVA STAGE IVB
  6Q GAIN MUTATED          11         1
  6Q GAIN WILD-TYPE        15         1
D12V4, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 3                33
  STAGE IIA               20               153
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                5                21
  STAGE IIIA               5                13
  STAGE IIIB              19                64
  STAGE IIIC              14                40
  STAGE IV                13                50
  STAGE IVA               11                15
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     4  17  75  15
  6Q GAIN WILD-TYPE  16  89 342  52
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                16
  T2              17                89
  T3              75               342
  T4              15                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6Q GAIN MUTATED    48  29  33
  6Q GAIN WILD-TYPE 297 121  82
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              48               297
  N1              29               121
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    72  24
  6Q GAIN WILD-TYPE 378  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     72   24
  6Q GAIN WILD-TYPE  378   64
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              72               378
  1              24                64
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    49  62
  6Q GAIN WILD-TYPE 238 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     49   62
  6Q GAIN WILD-TYPE  238  263
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              49               238
  MALE                62               263
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    75   9
  6Q GAIN WILD-TYPE 371  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     75    9
  6Q GAIN WILD-TYPE  371   19
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               75               371
  YES               9                19
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                     67                             8
  6Q GAIN WILD-TYPE                  315                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                      34                              0
  6Q GAIN WILD-TYPE                   112                             13
D12V10, multiclass
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        67               315
  COLON MUCINOUS ADENOCARCINOMA                8                52
  RECTAL ADENOCARCINOMA                       34               112
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    81   0  10   4
  6Q GAIN WILD-TYPE 361   5  27  25
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              81               361
  R1               0                 5
  R2              10                27
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          14    57
  6Q GAIN WILD-TYPE                        50   235
D12V13, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     14                50
  WHITE                                         57               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  67
  6Q GAIN WILD-TYPE   5 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   67
  6Q GAIN WILD-TYPE    5  281
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              67               281
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   267  70
  7P GAIN WILD-TYPE 205  51
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              337               256 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               70                51 
$`7P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80        12.66         1.61        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 
       43.43        44.91        35.11        45.60        13.94        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       30.44        29.19        29.16        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        20.61        24.69        23.87        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 
        1.02        37.05         1.02        35.01        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 
       38.99         9.07        36.03         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 
       12.99        14.01        33.99        13.02        24.00        19.99 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        85.05        10.06        35.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        14.93         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       31.00        24.00        24.00        20.98        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        26.01        27.02        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       34.03        38.04        42.02         1.02        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       33.04        26.01        51.98         2.01         5.03         0.92 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       39.98        40.96        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42         0.20        16.44        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.95        33.01        17.82        17.26        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       75.95       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 
        3.06         2.14         3.25         3.29        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
      148.01        85.45         9.99        20.02        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       27.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.08        11.01        10.06        19.59        55.92 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
        4.80        10.26        24.43        38.20        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 
       12.59         7.50        44.32       131.51         7.76         6.12 
TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       14.04        35.97       117.07        95.18         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       35.74         1.55        33.67         0.53        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       28.21        82.39        23.51        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        13.78        91.79        46.75        74.79        18.18 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-QL-A97D 
        9.93        15.65        12.79        17.85         8.42        21.90 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3911 
       30.28        70.03        24.13        39.48        17.23        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       10.39        14.50        16.83        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       65.98         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       13.94        19.99        20.98        29.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.99        17.95        17.03        35.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H 
       19.99        36.03         1.02        17.03        46.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03         1.94        38.96        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
        0.72        26.43        10.19         6.05         9.37         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        11.01         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        27.95        10.98         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
      126.44        41.36        57.24       129.27        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.31        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`7P GAIN WILD-TYPE`
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        9.53        39.45        46.65        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       16.57        37.05        14.53        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       22.06        32.71        27.09         8.38        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 
       20.12        19.66        61.84         3.02        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
       13.02         1.02        24.03        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
       19.07        34.03        29.00         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3672 
       29.95        23.01        20.98        13.94         6.97         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       50.04        47.05        47.01        26.99        19.04        19.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 
       17.03        10.06         0.00        33.07        36.03        31.07 
TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
       53.00         2.01        12.99        33.01        26.01         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 
       34.03         2.01        50.99        13.05        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       19.07         7.96        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       34.98        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 
        2.96        39.98        22.03        41.00        18.05         0.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72        10.88         0.46         0.92        27.09 
TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       21.44        17.85        19.33        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 
       32.94         5.13         6.77       100.01        11.74        12.69 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
        0.07        12.20        12.76        10.06        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       23.05        37.02        26.04        30.08        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       21.99        13.02        14.04        12.95        13.05        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       45.40        12.26        56.09        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       17.85        16.14        15.58         3.68         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 
        1.51        12.00        11.38       119.70       130.65        13.32 
TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      140.38       135.65       139.17        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24        11.11        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 
       34.42        41.42        16.24        13.25        35.31         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       67.30        53.62        85.48        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 
       26.17        79.69        10.98        19.33        19.33        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-AF-2691 
       42.77        29.46        32.98        31.30        11.90        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       13.55        19.10        34.49        10.39        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
       12.00        32.02         8.02        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        2.01        50.04         7.99         0.99        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 
       19.04         1.02        36.95        13.02        14.01        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         3.98        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       23.01        37.02        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
       61.97        41.00         1.45         1.81        33.17         6.97 
TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DG 
       12.39        15.02        13.97        19.99         5.95        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 
       32.61        20.55        19.96        17.00        16.41         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       17.46        49.51         0.53         1.12 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           148.01            140.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           19.990            20.085 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   244 102
  7P GAIN WILD-TYPE 202  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    244  102
  7P GAIN WILD-TYPE  202   60
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON              244               202
  RECTUM             102                60
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7P GAIN MUTATED        57        1       18        74         3         2
  7P GAIN WILD-TYPE      47        0       18        99         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          14         12         61         36       42
  7P GAIN WILD-TYPE        12          6         22         18       21
                   vv
clus                STAGE IVA STAGE IVB
  7P GAIN MUTATED          18         1
  7P GAIN WILD-TYPE         8         1
D13V4, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 57                47
  STAGE IA                 1                 0
  STAGE II                18                18
  STAGE IIA               74                99
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III               14                12
  STAGE IIIA              12                 6
  STAGE IIIB              61                22
  STAGE IIIC              36                18
  STAGE IV                42                21
  STAGE IVA               18                 8
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    13  60 235  38
  7P GAIN WILD-TYPE   7  46 182  29
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              13                 7
  T2              60                46
  T3             235               182
  T4              38                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7P GAIN MUTATED   168 103  75
  7P GAIN WILD-TYPE 177  47  40
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             168               177
  N1             103                47
  N2              75                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   242  59
  7P GAIN WILD-TYPE 208  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    242   59
  7P GAIN WILD-TYPE  208   29
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             242               208
  1              59                29
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   160 188
  7P GAIN WILD-TYPE 127 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    160  188
  7P GAIN WILD-TYPE  127  137
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             160               127
  MALE               188               137
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   252  18
  7P GAIN WILD-TYPE 194  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    252   18
  7P GAIN WILD-TYPE  194   10
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              252               194
  YES              18                10
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                    219                            24
  7P GAIN WILD-TYPE                  163                            36
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                      98                              3
  7P GAIN WILD-TYPE                    48                             10
D13V10, multiclass
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       219               163
  COLON MUCINOUS ADENOCARCINOMA               24                36
  RECTAL ADENOCARCINOMA                       98                48
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   250   4  24  14
  7P GAIN WILD-TYPE 192   1  13  15
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             250               192
  R1               4                 1
  R2              24                13
  RX              14                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     6
  7P GAIN WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          41   176
  7P GAIN WILD-TYPE                        23   116
D13V13, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                 6
  BLACK OR AFRICAN AMERICAN                     41                23
  WHITE                                        176               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"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2 209
  7P GAIN WILD-TYPE   3 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  209
  7P GAIN WILD-TYPE    3  139
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             209               139
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   240  60
  7Q GAIN WILD-TYPE 232  61
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              300               293 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               60                61 
$`7Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 
       15.62        12.66         1.61        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       35.11        45.60        13.94        37.25        37.02        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 
       32.91        31.63        30.44        29.19        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       24.13        25.08        25.18        24.16        20.61        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        16.24        24.92         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3538 
        6.97        38.99         9.07        36.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 
       12.99        14.01        33.99        13.02        24.00        19.99 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08         6.05         2.01        14.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 
        0.00        32.05         0.99        31.07        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 
       29.98        18.05        31.00        24.00        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       21.99        16.08        34.06        27.02        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       19.00        34.03        42.02         1.02        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       33.04        26.01        51.98         2.01         5.03         0.92 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       39.98        40.96        15.52         0.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.20        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 
       17.82        17.26        18.84       109.28        75.95       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        88.21        49.41        12.10 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6719 
        5.23         3.19         3.06         2.14         3.25        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56       148.01        85.45         9.99        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        27.02        13.02        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.08        11.01        10.06        19.59        55.92 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 
       12.49         1.48         4.41        12.43        14.30         4.80 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51         7.76         6.12        14.04 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 
       95.18         8.61        31.96        35.74         1.55        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
        0.53        47.41       133.18        82.39        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       65.85        44.68        55.04        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        26.43        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       74.79        18.18         9.93        15.65        12.79        17.85 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        21.90        30.28        70.03        24.13        39.48 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       10.39        14.50        16.83        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3592 
       65.98         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       20.98        29.98         0.99         0.99        19.99        17.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       17.03        35.01         1.02        48.03        19.99        28.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        1.02        46.03        25.97        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A032 
        1.02        12.00        31.00        70.03        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
       38.56         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        9.37        78.12         7.17        21.01        11.01         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
        8.98        15.02        27.95        10.98         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6508 
        5.29        41.36        57.24        24.13         0.49        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
       18.28        15.85        17.69        16.34        16.31        11.51 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         9.96        31.30        28.57         0.39        32.19 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76        12.46        55.76        47.08        26.43 

$`7Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         9.53        39.45        46.65        43.76        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 
       24.33        42.28        16.57        37.05        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       14.53        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        21.76        24.39        20.12        19.66 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
       61.84        56.25         3.02        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
       19.07        34.03        29.00         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 
       29.95        23.01        20.98        13.94         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3688 TCGA-AA-3710 
        0.92        50.04        47.05        47.01        19.00        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04        10.06        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 
       33.07        36.03        31.07        53.00        17.03         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       12.99        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       50.99        13.05        26.01        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
        7.96        38.04        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       34.98        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 
        2.96        39.98        22.03        41.00        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AM-5821 
       21.37        56.55         0.72         5.79        10.88         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       27.09        33.01        21.44        17.85        19.33        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6601 
        1.41         5.65        32.94         5.13         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 
       29.56        11.74         1.61        12.69         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       12.20        12.76        10.06        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       37.02        26.04        29.06        30.08        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       21.99        13.02        14.04        12.95        13.05        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       45.40        12.26        56.09        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 
       17.85        16.14        15.58         3.68         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      130.65       140.38       135.65       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6461 
      119.93        35.97        60.79       117.07        98.24        11.11 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 
       13.25        35.31        28.21         8.35        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       85.48        22.09        26.04        35.80        26.17        79.69 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98        19.33        19.33        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       32.98        31.30        11.90        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       19.10        34.49        37.74        10.39        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3591 
       12.00        32.02         8.02        20.05         1.02        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01        50.04         6.05         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       37.02        32.98        19.04         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 
       14.01        32.02        36.03        14.04        17.03         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y 
       20.98        13.94         6.02        23.01        37.02        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.97         1.94        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.45         1.81        33.17         6.97         4.73        12.39 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        13.97        19.99         5.95       126.44       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       51.48        32.61         2.40        20.55        19.96        17.00 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       16.41         8.61        10.78        13.64        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
       49.51         0.66         0.53         1.12        18.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           148.01            140.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            19.99             20.19 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   222  86
  7Q GAIN WILD-TYPE 224  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    222   86
  7Q GAIN WILD-TYPE  224   76
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON              222               224
  RECTUM              86                76
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q GAIN MUTATED        54        1       16        63         3         1
  7Q GAIN WILD-TYPE      50        0       20       110         7         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          13          8         56         31       38
  7Q GAIN WILD-TYPE        13         10         27         23       25
                   vv
clus                STAGE IVA STAGE IVB
  7Q GAIN MUTATED          17         1
  7Q GAIN WILD-TYPE         9         1
D14V4, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 54                50
  STAGE IA                 1                 0
  STAGE II                16                20
  STAGE IIA               63               110
  STAGE IIB                3                 7
  STAGE IIC                1                 2
  STAGE III               13                13
  STAGE IIIA               8                10
  STAGE IIIB              56                27
  STAGE IIIC              31                23
  STAGE IV                38                25
  STAGE IVA               17                 9
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    13  52 209  34
  7Q GAIN WILD-TYPE   7  54 208  33
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              13                 7
  T2              52                54
  T3             209               208
  T4              34                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7Q GAIN MUTATED   152  90  66
  7Q GAIN WILD-TYPE 193  60  49
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             152               193
  N1              90                60
  N2              66                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   211  55
  7Q GAIN WILD-TYPE 239  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    211   55
  7Q GAIN WILD-TYPE  239   33
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             211               239
  1              55                33
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   143 167
  7Q GAIN WILD-TYPE 144 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    143  167
  7Q GAIN WILD-TYPE  144  158
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             143               144
  MALE               167               158
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   226  14
  7Q GAIN WILD-TYPE 220  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    226   14
  7Q GAIN WILD-TYPE  220   14
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              226               220
  YES              14                14
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                    198                            22
  7Q GAIN WILD-TYPE                  184                            38
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                      83                              2
  7Q GAIN WILD-TYPE                    63                             11
D14V10, multiclass
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       198               184
  COLON MUCINOUS ADENOCARCINOMA               22                38
  RECTAL ADENOCARCINOMA                       83                63
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   223   3  23  14
  7Q GAIN WILD-TYPE 219   2  14  15
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             223               219
  R1               3                 2
  R2              23                14
  RX              14                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     5
  7Q GAIN WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          38   154
  7Q GAIN WILD-TYPE                        26   138
D14V13, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 7
  BLACK OR AFRICAN AMERICAN                     38                26
  WHITE                                        154               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 184
  7Q GAIN WILD-TYPE   3 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  184
  7Q GAIN WILD-TYPE    3  164
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             184               164
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   127  35
  8P GAIN WILD-TYPE 345  86
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              162               431 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35                86 
$`8P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2677 TCGA-A6-2682 
       15.62        12.66         1.61        39.45        24.33        13.94 
TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       37.02        32.45        31.63        29.19        32.71        29.16 
TCGA-A6-6649 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       24.16         9.63         1.02        35.01         6.97         1.02 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       36.03        19.07        29.00        29.00        12.99        14.01 
TCGA-AA-3558 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3696 
       20.98         6.05         6.97        14.01        50.04         5.03 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 
       19.04        19.04        10.06        17.03         0.00        31.07 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-A00K TCGA-AA-A00R 
       29.98        18.05        12.99         2.01        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O 
       17.03        10.98        51.98         2.96         5.03         0.92 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-6197 
        0.07         5.79        27.42        16.44        27.09        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       17.26        18.84        32.94         5.13        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       88.21        49.41         5.23         3.19        12.69         3.06 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
        2.14         0.07       148.01        51.32         1.91        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 
       37.02        25.02         8.02        27.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 
       15.02        17.03        15.02        29.03        14.99        12.99 
TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6537 
       11.08        55.92        20.19        17.75         1.32         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-7000 
       17.13        16.14         1.48        12.43        14.30        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F 
      119.70        24.43        38.20         7.50        44.32        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 
      117.07        98.24         8.61        35.74         6.18        16.24 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 
        8.35        67.30        65.85        53.62        44.68        63.62 
TCGA-G4-6311 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YW 
       39.42        46.75        74.79        18.18        15.65        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-6655 
       32.98         8.42        70.03        43.04        34.49        20.02 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3598 TCGA-AG-3731 TCGA-AG-3881 
       65.98        36.03        32.02        50.04        37.02        19.04 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 
       36.95         1.02        48.03        32.02         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A032 
       46.03         9.07        31.00        70.03        64.01        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-6156 
       38.56         0.69         6.05         9.37         7.17        15.02 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 
        4.01        41.36        57.24        24.13         0.49        17.00 
TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6572 
       16.31        11.51        49.51         0.39         0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80         9.53        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       42.90        42.28        44.91        35.11        45.60        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       30.44        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       20.28        16.24        24.92        61.84        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 
        7.04         3.02        37.05         1.02        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 
        8.05         0.00        19.07        34.03        26.01         0.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       11.01         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 
       31.07        53.00        17.03        24.03        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        10.88         0.20         0.46         0.92        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
       16.31         0.95        33.01        17.82        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4681 
      109.28        75.95        58.39         1.41         5.65       106.75 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       62.79         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        1.61         3.25         3.29        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56        85.45        70.16        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
        9.99        21.14        82.95       124.27        23.05        26.04 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
        5.03        12.00         2.96        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        20.42        18.25        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       12.49        15.58         3.68         4.41         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D0 
       11.64         4.80         1.51        12.00        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       81.37       119.93        60.79        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       35.74        47.87         1.55        34.42        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       82.39        23.51        74.56        55.04        85.48        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       35.80        26.17        91.79        79.69        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        12.79        17.85        16.80        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
       31.30        21.90        30.28        11.90        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        13.55        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       16.83        15.39        10.39        86.63        11.84        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       46.03        34.03        34.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        17.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 
       37.02        15.95        36.03         1.02        12.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        1.45         0.72        26.43         1.81        10.19        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        6.97         4.73        12.39        78.12        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       15.02         5.03         8.98        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       19.99         5.95         5.03         5.29       126.44       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30        28.57        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.12        12.46        18.28        55.76        26.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           148.01            140.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            18.51             20.42 
[1] "0.0 - 148.0 (18.5)" "0.0 - 140.4 (20.4)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   130  40
  8P GAIN WILD-TYPE 316 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    130   40
  8P GAIN WILD-TYPE  316  122
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON              130               316
  RECTUM              40               122
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P GAIN MUTATED        28        0       14        48         3         2
  8P GAIN WILD-TYPE      76        1       22       125         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           5          2         22         16       21
  8P GAIN WILD-TYPE        21         16         61         38       42
                   vv
clus                STAGE IVA STAGE IVB
  8P GAIN MUTATED           6         0
  8P GAIN WILD-TYPE        20         2
D15V4, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 28                76
  STAGE IA                 0                 1
  STAGE II                14                22
  STAGE IIA               48               125
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III                5                21
  STAGE IIIA               2                16
  STAGE IIIB              22                61
  STAGE IIIC              16                38
  STAGE IV                21                42
  STAGE IVA                6                20
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED     5  27 120  17
  8P GAIN WILD-TYPE  15  79 297  50
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               5                15
  T2              27                79
  T3             120               297
  T4              17                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8P GAIN MUTATED   103  34  32
  8P GAIN WILD-TYPE 242 116  83
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             103               242
  N1              34               116
  N2              32                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   120  28
  8P GAIN WILD-TYPE 330  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    120   28
  8P GAIN WILD-TYPE  330   60
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             120               330
  1              28                60
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    80  90
  8P GAIN WILD-TYPE 207 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     80   90
  8P GAIN WILD-TYPE  207  235
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              80               207
  MALE                90               235
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   119   7
  8P GAIN WILD-TYPE 327  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    119    7
  8P GAIN WILD-TYPE  327   21
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              119               327
  YES               7                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                    115                            14
  8P GAIN WILD-TYPE                  267                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                      36                              3
  8P GAIN WILD-TYPE                   110                             10
D15V10, multiclass
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       115               267
  COLON MUCINOUS ADENOCARCINOMA               14                46
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   114   0  14  12
  8P GAIN WILD-TYPE 328   5  23  17
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             114               328
  R1               0                 5
  R2              14                23
  RX              12                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     4
  8P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          20    90
  8P GAIN WILD-TYPE                        44   202
D15V13, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 8
  BLACK OR AFRICAN AMERICAN                     20                44
  WHITE                                         90               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2 105
  8P GAIN WILD-TYPE   3 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  105
  8P GAIN WILD-TYPE    3  243
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             105               243
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   235  67
  8Q GAIN WILD-TYPE 237  54
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              302               291 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               67                54 
$`8Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2675 
       15.62        12.66         1.61         9.53        39.45        43.43 
TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 
       24.33        35.11        45.60        13.94        37.25        37.02 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        31.63        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       32.71        29.16        27.09        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       24.16        24.69        23.87         9.63         5.03         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 
       37.05         1.02        35.01         6.97         1.02        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       14.01        33.99        13.02        24.00        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       50.04        47.01        15.02         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
        5.03        19.04        19.04        10.06        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       17.03         0.00         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3956 
       27.02        29.98        18.05         2.01        12.99        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A004 
        2.01        16.08        34.06        26.01        24.00        13.94 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01G 
       19.00        18.05         0.99        17.03        10.98        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J 
       31.00         1.02        37.02        51.98         2.96         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6963 
        0.92        41.00         0.07        15.52         5.79        27.42 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L 
       16.44         0.92        27.09        16.31        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       18.84       109.28        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        88.21        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
        0.07        10.06        14.30       148.01        15.62        51.32 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
        1.91        20.02        37.02        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 
       15.02        15.02        17.03        15.02        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5540 TCGA-D5-5541 
       14.99        12.99        13.02        11.08        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        17.75         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04         4.80        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       24.43        38.20       130.65       140.38         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
       31.96        35.74        35.74         6.18        34.42        16.24 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        63.62        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       26.43        46.75        74.79        18.18        10.98         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       15.65        16.80        29.46        32.98         8.42        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        10.39        20.02        10.39        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02        36.03        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 
       34.03        34.03        50.04         6.05         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3896 
        7.99        37.02        32.98        19.04        36.95         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        3.98        46.03        25.97        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
        1.02        31.00        70.03        64.01        51.98         1.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       38.04        38.56         1.45         0.69        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        9.37         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       15.02        10.98         4.01         5.03       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 
       57.24        24.13        32.61         0.49        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
       16.31        11.51        10.78        13.64         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
       28.57         0.39        32.19         0.76        12.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`8Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        4.80        43.76        46.65        43.76        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 
       44.91        16.57        37.05        34.65        14.53        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 
       33.53        22.09        22.06        22.52         8.38        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 
       24.92        61.84        56.25         7.04         3.02        58.03 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 
       37.05         8.05        19.07        34.03         0.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 
       17.95        29.95        19.99        13.94        61.02         2.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 
        0.92        47.05        11.01        19.00        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 
       36.03        32.05        31.07        53.00        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       33.01        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       50.99        13.05        25.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       27.02        38.04        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01        27.02        42.02        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        1.02        15.02        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02F 
       35.01        33.04        35.01        26.01        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        2.01        22.03        39.98        18.05        40.96        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72        22.42        10.88         0.20 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        33.01        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-5403 
       19.33        75.95        58.39         1.41         5.65        62.79 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        6.77       100.01         3.25         3.29        12.20        12.76 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56        85.45        70.16        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5860 
       82.95       124.27        23.05        26.04        22.03        32.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       12.00         2.96        16.04        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 
       45.40        12.26        19.59        20.42        18.25        17.85 
TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.49         3.68         9.44        11.64         1.51        12.00 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        47.87         1.55        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        85.48        61.91        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        79.69        19.33        19.33 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       12.79        17.85        42.77        31.30        21.90        11.90 
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N 
       19.10        14.50        16.83        15.39        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 
       12.00         8.02         7.07        20.05        34.03         2.01 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3727 
       12.03        15.95        19.99        13.94        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       29.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-4001 
       17.03        13.02        35.01        14.01        19.99        36.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L 
       20.98        13.94         6.02        23.01        36.03        12.00 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6644 
       10.98        49.97        38.96        61.97        41.00         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 
       26.43         1.81        33.17         6.97        12.39        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02         8.98        27.95        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
        5.29       129.27        51.48         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 
       20.91        18.28        15.85        17.69        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 
       17.46        11.97         8.45        31.30         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
        0.53         1.12        18.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           148.01            139.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            20.02             19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   226  87
  8Q GAIN WILD-TYPE 220  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    226   87
  8Q GAIN WILD-TYPE  220   75
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON              226               220
  RECTUM              87                75
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q GAIN MUTATED        45        0       21        85         3         2
  8Q GAIN WILD-TYPE      59        1       15        88         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          11         11         41         33       44
  8Q GAIN WILD-TYPE        15          7         42         21       19
                   vv
clus                STAGE IVA STAGE IVB
  8Q GAIN MUTATED          13         0
  8Q GAIN WILD-TYPE        13         2
D16V4, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 45                59
  STAGE IA                 0                 1
  STAGE II                21                15
  STAGE IIA               85                88
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III               11                15
  STAGE IIIA              11                 7
  STAGE IIIB              41                42
  STAGE IIIC              33                21
  STAGE IV                44                19
  STAGE IVA               13                13
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED     6  52 222  33
  8Q GAIN WILD-TYPE  14  54 195  34
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               6                14
  T2              52                54
  T3             222               195
  T4              33                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8Q GAIN MUTATED   168  75  70
  8Q GAIN WILD-TYPE 177  75  45
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             168               177
  N1              75                75
  N2              70                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   220  57
  8Q GAIN WILD-TYPE 230  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    220   57
  8Q GAIN WILD-TYPE  230   31
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             220               230
  1              57                31
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   146 168
  8Q GAIN WILD-TYPE 141 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    146  168
  8Q GAIN WILD-TYPE  141  157
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             146               141
  MALE               168               157
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   224  17
  8Q GAIN WILD-TYPE 222  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    224   17
  8Q GAIN WILD-TYPE  222   11
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              224               222
  YES              17                11
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                    202                            22
  8Q GAIN WILD-TYPE                  180                            38
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                      81                              4
  8Q GAIN WILD-TYPE                    65                              9
D16V10, multiclass
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       202               180
  COLON MUCINOUS ADENOCARCINOMA               22                38
  RECTAL ADENOCARCINOMA                       81                65
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   214   3  27  17
  8Q GAIN WILD-TYPE 228   2  10  12
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             214               228
  R1               3                 2
  R2              27                10
  RX              17                12
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     6
  8Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          35   157
  8Q GAIN WILD-TYPE                        29   135
D16V13, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                 6
  BLACK OR AFRICAN AMERICAN                     35                29
  WHITE                                        157               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 187
  8Q GAIN WILD-TYPE   2 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  187
  8Q GAIN WILD-TYPE    2  161
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             187               161
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    85  33
  9P GAIN WILD-TYPE 387  88
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              118               475 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               33                88 
$`9P GAIN MUTATED`
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-5657 
        1.61        43.76        44.91        13.94        37.02        31.63 
TCGA-A6-6142 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3520 
       25.08        20.28        16.24        56.25         5.03        24.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3660 
       29.00        29.00        14.01        33.99        20.98        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3852 
        6.97         2.01        50.04        14.93        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3976 TCGA-AA-3994 TCGA-AA-A00Q 
       36.03         0.99        27.02        26.01        27.02        42.02 
TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 
       21.99        15.02        10.98        51.98         5.79        22.42 
TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-6600 TCGA-AZ-6603 
       16.44        33.01        17.26        75.95        12.10        29.56 
TCGA-CA-5796 TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        3.25         9.99        13.02        22.03         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6531 
       17.03         2.96        29.03        14.99        19.59        17.75 
TCGA-D5-6539 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 
       12.49        11.64         4.80        12.59         7.50         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       14.04        26.47        98.24        95.18         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
        6.18         1.55        13.78        91.79        46.75        10.98 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2689 
       12.79        17.85        42.77        21.90        70.03        39.48 
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       17.23        34.49        20.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        2.01        50.04         0.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 
        7.99         0.99        19.04        17.03         1.02        32.02 
TCGA-AG-4001 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6643 
       36.03        70.03        10.98        51.98        38.04         0.69 
TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 
        0.72        21.01        27.95       129.27         2.40        11.51 
TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 
       10.78         8.45         9.96        28.57         0.39         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        1.12        12.46        18.28        26.43 

$`9P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80        12.66         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       45.60        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       14.53        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13         8.38        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 
        1.02        13.02        38.99         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99         0.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       61.02         6.05        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        33.07        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98         1.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
       33.04        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        8.02        27.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        12.26        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.04         9.44         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65         7.76       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        11.11        35.74        35.74        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        26.04        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        79.69        18.18        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        16.80        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        11.90        24.13        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       37.74        10.39        14.50        16.83        15.39        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 
       34.03        12.03         6.05        15.95        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02        32.98         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       17.95        36.95        13.02        35.01        14.01        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       19.99        28.04        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        64.01        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       41.00        38.56         1.45        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        15.02        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       16.41         8.61        13.64        17.46        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 
       31.30        32.19         0.66         0.53         0.76        55.76 
TCGA-G5-6572 
       47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            148.01 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            17.80             20.19 
[1] "0.0 - 129.3 (17.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    80  42
  9P GAIN WILD-TYPE 366 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     80   42
  9P GAIN WILD-TYPE  366  120
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON               80               366
  RECTUM              42               120
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P GAIN MUTATED        15        1        7        31         2         2
  9P GAIN WILD-TYPE      89        0       29       142         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           3          8         12         17       12
  9P GAIN WILD-TYPE        23         10         71         37       51
                   vv
clus                STAGE IVA STAGE IVB
  9P GAIN MUTATED           7         1
  9P GAIN WILD-TYPE        19         1
D17V4, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 15                89
  STAGE IA                 1                 0
  STAGE II                 7                29
  STAGE IIA               31               142
  STAGE IIB                2                 8
  STAGE IIC                2                 1
  STAGE III                3                23
  STAGE IIIA               8                10
  STAGE IIIB              12                71
  STAGE IIIC              17                37
  STAGE IV                12                51
  STAGE IVA                7                19
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     3  17  85  16
  9P GAIN WILD-TYPE  17  89 332  51
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               3                17
  T2              17                89
  T3              85               332
  T4              16                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9P GAIN MUTATED    62  31  28
  9P GAIN WILD-TYPE 283 119  87
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              62               283
  N1              31               119
  N2              28                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    85  19
  9P GAIN WILD-TYPE 365  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     85   19
  9P GAIN WILD-TYPE  365   69
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              85               365
  1              19                69
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    59  63
  9P GAIN WILD-TYPE 228 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     59   63
  9P GAIN WILD-TYPE  228  262
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              59               228
  MALE                63               262
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    84   6
  9P GAIN WILD-TYPE 362  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     84    6
  9P GAIN WILD-TYPE  362   22
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               84               362
  YES               6                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                     62                            18
  9P GAIN WILD-TYPE                  320                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                      36                              5
  9P GAIN WILD-TYPE                   110                              8
D17V10, multiclass
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        62               320
  COLON MUCINOUS ADENOCARCINOMA               18                42
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    95   0   6   3
  9P GAIN WILD-TYPE 347   5  31  26
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              95               347
  R1               0                 5
  R2               6                31
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  1     1
  9P GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          18    55
  9P GAIN WILD-TYPE                        46   237
D17V13, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     18                46
  WHITE                                         55               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  66
  9P GAIN WILD-TYPE   3 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   66
  9P GAIN WILD-TYPE    3  282
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              66               282
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    69  29
  9Q GAIN WILD-TYPE 403  92
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               98               495 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               29                92 
$`9Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-A565 
       43.76        44.91        13.94        37.02        31.63        16.24 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
       56.25         5.03        29.00        29.00        14.01        33.99 
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3844 
       20.98        78.08         6.97         2.01        50.04        14.93 
TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 
       10.06         0.00        36.03         0.99        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 
       13.94        42.02        21.99        15.02        10.98        51.98 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-A54L TCGA-AZ-4313 
        5.79        22.42        16.44        33.01        17.26        75.95 
TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-5914 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       12.10         3.25         9.99         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6928 
        2.96        29.03        14.99        17.75        12.49        11.64 
TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        4.80        12.59         7.50         6.12        14.04        26.47 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6323 TCGA-G4-6625 
       98.24        95.18        31.96         6.18        13.78        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QL-A97D TCGA-WS-AB45 
       46.75        10.98        12.79        17.85        21.90        70.03 
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       39.48        34.49        20.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3878 TCGA-AG-3881 
       50.04         0.99        13.94        20.98         0.99        19.04 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 
       17.03         1.02        32.02        10.98        51.98        38.04 
TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 
        0.72        21.01        27.95       129.27         2.40        11.51 
TCGA-EI-6884 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
       10.78         9.96         0.39         0.69         1.12        12.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`9Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        45.60        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       20.12        19.66        20.28        24.92        61.84         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        19.07        34.03        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       36.95        37.02         0.00        17.03         0.00        33.07 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       32.02        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       44.32       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 
      119.93        35.97        60.79       117.07         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        26.04        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       18.18        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        30.28 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       11.90        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       37.74        10.39        14.50        16.83        15.39        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       46.03        34.03        12.03         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.56         1.45         0.69        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        15.02        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.41         8.61        13.64        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       49.51        31.30        28.57        32.19         0.66         0.53 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 0 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            148.01 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.03             20.28 
[1] "0.0 - 129.3 (17.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    69  32
  9Q GAIN WILD-TYPE 377 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     69   32
  9Q GAIN WILD-TYPE  377  130
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON               69               377
  RECTUM              32               130
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q GAIN MUTATED        13        1        5        29         1         2
  9Q GAIN WILD-TYPE      91        0       31       144         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           3          6          9         13       11
  9Q GAIN WILD-TYPE        23         12         74         41       52
                   vv
clus                STAGE IVA STAGE IVB
  9Q GAIN MUTATED           4         1
  9Q GAIN WILD-TYPE        22         1
D18V4, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 1                 0
  STAGE II                 5                31
  STAGE IIA               29               144
  STAGE IIB                1                 9
  STAGE IIC                2                 1
  STAGE III                3                23
  STAGE IIIA               6                12
  STAGE IIIB               9                74
  STAGE IIIC              13                41
  STAGE IV                11                52
  STAGE IVA                4                22
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     3  13  71  13
  9Q GAIN WILD-TYPE  17  93 346  54
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               3                17
  T2              13                93
  T3              71               346
  T4              13                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9Q GAIN MUTATED    54  23  23
  9Q GAIN WILD-TYPE 291 127  92
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              54               291
  N1              23               127
  N2              23                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    71  16
  9Q GAIN WILD-TYPE 379  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     71   16
  9Q GAIN WILD-TYPE  379   72
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              71               379
  1              16                72
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    46  55
  9Q GAIN WILD-TYPE 241 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     46   55
  9Q GAIN WILD-TYPE  241  270
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              46               241
  MALE                55               270
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    68   5
  9Q GAIN WILD-TYPE 378  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     68    5
  9Q GAIN WILD-TYPE  378   23
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               68               378
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                     53                            16
  9Q GAIN WILD-TYPE                  329                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                      27                              4
  9Q GAIN WILD-TYPE                   119                              9
D18V10, multiclass
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        53               329
  COLON MUCINOUS ADENOCARCINOMA               16                44
  RECTAL ADENOCARCINOMA                       27               119
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    77   0   6   3
  9Q GAIN WILD-TYPE 365   5  31  26
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              77               365
  R1               0                 5
  R2               6                31
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          15    45
  9Q GAIN WILD-TYPE                        49   247
D18V13, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     15                49
  WHITE                                         45               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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  55
  9Q GAIN WILD-TYPE   5 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   55
  9Q GAIN WILD-TYPE    5  293
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              55               293
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    31  14
  10P GAIN WILD-TYPE 441 107
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                45                548 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                107 
$`10P GAIN MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-4107 
       12.66         1.61        39.45        43.76        37.02        32.45 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3548 TCGA-AA-3666 TCGA-AA-3845 
       24.16        20.61        20.28        33.99         2.01         0.00 
TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3952 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A8YK 
       33.07        27.02         2.01        16.31        17.26        18.84 
TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 
       12.69        32.02         5.03         2.96        11.01        19.59 
TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6459 
       56.09        43.27        14.30        12.59         7.50         8.61 
TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-G4-6625 TCGA-QL-A97D TCGA-AF-2689 
        1.55        74.56        36.00        91.79        21.90        39.48 
TCGA-AG-3902 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 
       32.02        15.95         9.07        70.03        10.19        21.01 
TCGA-DY-A1DF TCGA-F5-6571 TCGA-F5-6812 
       24.13        31.30         0.66 

$`10P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       15.62         4.80         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       13.94        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       14.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       22.52        24.13         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       27.42        10.88         0.20        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.26        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       37.02        36.03         1.02        12.00        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        12.39        78.12         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        28.57         0.39        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             91.79             148.01 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             20.28              19.99 
[1] "0.0 - 91.8 (20.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    38  11
  10P GAIN WILD-TYPE 408 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     38   11
  10P GAIN WILD-TYPE  408  151
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON                38                408
  RECTUM               11                151
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P GAIN MUTATED         5        0        1        16         1         0
  10P GAIN WILD-TYPE      99        1       35       157         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           2          1          5          8        6
  10P GAIN WILD-TYPE        24         17         78         46       57
                    vv
clus                 STAGE IVA STAGE IVB
  10P GAIN MUTATED           3         0
  10P GAIN WILD-TYPE        23         2
D19V4, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   5                 99
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                16                157
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                1                 17
  STAGE IIIB                5                 78
  STAGE IIIC                8                 46
  STAGE IV                  6                 57
  STAGE IVA                 3                 23
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     1   4  40   4
  10P GAIN WILD-TYPE  19 102 377  63
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 19
  T2                4                102
  T3               40                377
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10P GAIN MUTATED    24   9  16
  10P GAIN WILD-TYPE 321 141  99
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               24                321
  N1                9                141
  N2               16                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    32   9
  10P GAIN WILD-TYPE 418  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     32    9
  10P GAIN WILD-TYPE  418   79
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               32                418
  1                9                 79
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    23  26
  10P GAIN WILD-TYPE 264 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     23   26
  10P GAIN WILD-TYPE  264  299
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               23                264
  MALE                 26                299
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    34   1
  10P GAIN WILD-TYPE 412  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     34    1
  10P GAIN WILD-TYPE  412   27
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                34                412
  YES                1                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                     34                             4
  10P GAIN WILD-TYPE                  348                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                      11                              0
  10P GAIN WILD-TYPE                   135                             13
D19V10, multiclass
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         34                348
  COLON MUCINOUS ADENOCARCINOMA                 4                 56
  RECTAL ADENOCARCINOMA                        11                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    36   1   3   2
  10P GAIN WILD-TYPE 406   4  34  27
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               36                406
  R1                1                  4
  R2                3                 34
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1     1
  10P GAIN WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           8    26
  10P GAIN WILD-TYPE                        56   266
D19V13, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       8                 56
  WHITE                                          26                266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  32
  10P GAIN WILD-TYPE   3 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   32
  10P GAIN WILD-TYPE    3  316
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               32                316
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    21   6
  10Q GAIN WILD-TYPE 451 115
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                27                566 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                115 
$`10Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-4107 TCGA-AA-3666 TCGA-AA-3851 
       12.66         1.61        39.45        32.45         2.01        33.07 
TCGA-AA-3869 TCGA-AA-3982 TCGA-AA-A01R TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 
       27.02        27.02        35.01        17.26        18.84        12.69 
TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA 
       32.02        11.01        19.59        14.30        12.59         7.50 
TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QL-A97D TCGA-AF-2689 TCGA-AG-3999 
        1.55        74.56        36.00        21.90        39.48        28.04 
TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 
       70.03        10.19        21.01 

$`10Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       15.62         4.80         9.53        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.43        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.18        24.16        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       27.42        10.88         0.20        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.85        19.33       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       30.28        11.90        70.03        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        1.45         0.69         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.55               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             74.56             148.01 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             21.01              19.99 
[1] "1.6 - 74.6 (21.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    23   6
  10Q GAIN WILD-TYPE 423 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     23    6
  10Q GAIN WILD-TYPE  423  156
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON                23                423
  RECTUM                6                156
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q GAIN MUTATED         3        0        1         7         0         0
  10Q GAIN WILD-TYPE     101        1       35       166        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          1          4          5        3
  10Q GAIN WILD-TYPE        24         17         79         49       60
                    vv
clus                 STAGE IVA STAGE IVB
  10Q GAIN MUTATED           2         0
  10Q GAIN WILD-TYPE        24         2
D20V4, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                 7                166
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                1                 17
  STAGE IIIB                4                 79
  STAGE IIIC                5                 49
  STAGE IV                  3                 60
  STAGE IVA                 2                 24
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   3  24   2
  10Q GAIN WILD-TYPE  20 103 393  65
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                 20
  T2                3                103
  T3               24                393
  T4                2                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10Q GAIN MUTATED    12   8   9
  10Q GAIN WILD-TYPE 333 142 106
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               12                333
  N1                8                142
  N2                9                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    17   5
  10Q GAIN WILD-TYPE 433  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    5
  10Q GAIN WILD-TYPE  433   83
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               17                433
  1                5                 83
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    14  15
  10Q GAIN WILD-TYPE 273 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   15
  10Q GAIN WILD-TYPE  273  310
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                273
  MALE                 15                310
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    20   2
  10Q GAIN WILD-TYPE 426  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     20    2
  10Q GAIN WILD-TYPE  426   26
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                20                426
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                     19                             4
  10Q GAIN WILD-TYPE                  363                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                       6                              0
  10Q GAIN WILD-TYPE                   140                             13
D20V10, multiclass
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         19                363
  COLON MUCINOUS ADENOCARCINOMA                 4                 56
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    22   0   1   2
  10Q GAIN WILD-TYPE 420   5  36  27
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               22                420
  R1                0                  5
  R2                1                 36
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     1
  10Q GAIN WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           6    13
  10Q GAIN WILD-TYPE                        58   279
D20V13, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       6                 58
  WHITE                                          13                279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  17
  10Q GAIN WILD-TYPE   3 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   17
  10Q GAIN WILD-TYPE    3  331
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               17                331
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    66  18
  11P GAIN WILD-TYPE 406 103
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                84                509 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                103 
$`11P GAIN MUTATED`
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
        1.61        43.76        43.43        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3542 
       25.18        23.87        56.25         5.03         1.02        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3842 TCGA-AA-3846 
       13.02        24.00        19.99        50.04        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 
       33.07         0.99        24.03        18.05        20.98        27.02 
TCGA-AA-A00F TCGA-AA-A02F TCGA-AD-6888 TCGA-AD-6901 TCGA-AY-4070 TCGA-AY-4071 
       34.03        39.98        15.52        22.42        16.31         0.95 
TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CK-4948 
       18.84        65.00        62.79        29.56         1.61       148.01 
TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-6533 
        8.02        17.03        29.03        21.99        11.08         1.32 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6303 
       17.85         1.48         4.80        49.91        35.97        65.85 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2690 
       55.04        63.62        35.93        29.46        30.28        17.23 
TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3591 
       10.39        20.02        65.98        12.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4001 TCGA-AG-4007 
       34.03        19.99        13.94        19.99        36.03         1.02 
TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 
       25.97        31.00        26.43        10.19         9.37         4.73 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       11.01         5.03         8.98        27.95        19.99       126.44 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6233 
        2.40        16.31        13.64         0.39        32.19        18.28 

$`11P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80        12.66         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
       43.76        42.90        24.33        42.28        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84         9.63         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95        14.93         0.00        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       17.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        25.02        24.00        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       27.09        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13       106.75        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        12.00         2.96        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        42.77        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        37.74        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       10.39        86.63        11.84        36.03        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         1.81         6.05        33.17         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       12.39        78.12         7.17        21.01        15.02        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        10.98         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30        28.57         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        55.76        47.08        26.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            148.01             140.38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            21.485             19.960 
[1] "0.4 - 148.0 (21.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    53  31
  11P GAIN WILD-TYPE 393 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     53   31
  11P GAIN WILD-TYPE  393  131
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON                53                393
  RECTUM               31                131
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P GAIN MUTATED        13        0        3        18         1         1
  11P GAIN WILD-TYPE      91        1       33       155         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           1          4         13         10       13
  11P GAIN WILD-TYPE        25         14         70         44       50
                    vv
clus                 STAGE IVA STAGE IVB
  11P GAIN MUTATED           6         0
  11P GAIN WILD-TYPE        20         2
D21V4, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  13                 91
  STAGE IA                  0                  1
  STAGE II                  3                 33
  STAGE IIA                18                155
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 1                 25
  STAGE IIIA                4                 14
  STAGE IIIB               13                 70
  STAGE IIIC               10                 44
  STAGE IV                 13                 50
  STAGE IVA                 6                 20
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     4  16  61   4
  11P GAIN WILD-TYPE  16  90 356  63
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 16
  T2               16                 90
  T3               61                356
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11P GAIN MUTATED    41  23  21
  11P GAIN WILD-TYPE 304 127  94
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               41                304
  N1               23                127
  N2               21                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    56  19
  11P GAIN WILD-TYPE 394  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     56   19
  11P GAIN WILD-TYPE  394   69
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               56                394
  1               19                 69
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    39  46
  11P GAIN WILD-TYPE 248 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     39   46
  11P GAIN WILD-TYPE  248  279
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               39                248
  MALE                 46                279
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    61   5
  11P GAIN WILD-TYPE 385  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     61    5
  11P GAIN WILD-TYPE  385   23
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                61                385
  YES                5                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                     51                             2
  11P GAIN WILD-TYPE                  331                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                      31                              0
  11P GAIN WILD-TYPE                   115                             13
D21V10, multiclass
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         51                331
  COLON MUCINOUS ADENOCARCINOMA                 2                 58
  RECTAL ADENOCARCINOMA                        31                115
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    60   1   6   2
  11P GAIN WILD-TYPE 382   4  31  27
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               60                382
  R1                1                  4
  R2                6                 31
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                          11    46
  11P GAIN WILD-TYPE                        53   246
D21V13, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                      11                 53
  WHITE                                          46                246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  54
  11P GAIN WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   54
  11P GAIN WILD-TYPE    4  294
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               54                294
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    63  13
  11Q GAIN WILD-TYPE 409 108
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                76                517 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                108 
$`11Q GAIN MUTATED`
TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6142 
        1.61        43.43        44.91        29.19        29.16        25.08 
TCGA-A6-6648 TCGA-A6-A56B TCGA-AA-3494 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3552 
       25.18        56.25         1.02        29.00        12.99        13.02 
TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3846 
       24.00        19.99        50.04        37.05        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3955 
       10.06        33.07         0.99        31.07        24.03        20.98 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 
       27.02        34.03        16.31        18.84        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 
       29.56         1.61       148.01         8.02        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6898 TCGA-D5-6929 
       21.99        11.08        55.92         1.32         1.48         4.80 
TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 
       12.59        35.97        65.85        55.04        63.62        35.93 
TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-A56L TCGA-AG-3575 
       29.46        30.28        17.23        10.39        65.98        12.00 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3612 TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 
       46.03        34.03        19.99         1.02        36.03         1.02 
TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
       25.97        31.00        26.43         9.37         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6514 
        5.03         8.98        15.02        27.95       126.44        16.31 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       13.64         0.39        32.19         0.66 

$`11Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       38.99        36.95        14.93         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
        2.96        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        17.75        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       15.65        12.79        17.85        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30        21.90        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       13.94        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97        12.39        78.12         7.17        21.01        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 
        9.96        49.51        31.30        28.57         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            148.01             140.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            24.555             19.960 
[1] "0.4 - 148.0 (24.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    51  26
  11Q GAIN WILD-TYPE 395 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     51   26
  11Q GAIN WILD-TYPE  395  136
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON                51                395
  RECTUM               26                136
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q GAIN MUTATED        12        0        4        15         1         0
  11Q GAIN WILD-TYPE      92        1       32       158         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           1          3         12         10       10
  11Q GAIN WILD-TYPE        25         15         71         44       53
                    vv
clus                 STAGE IVA STAGE IVB
  11Q GAIN MUTATED           7         0
  11Q GAIN WILD-TYPE        19         2
D22V4, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  12                 92
  STAGE IA                  0                  1
  STAGE II                  4                 32
  STAGE IIA                15                158
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                3                 15
  STAGE IIIB               12                 71
  STAGE IIIC               10                 44
  STAGE IV                 10                 53
  STAGE IVA                 7                 19
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     2  16  54   5
  11Q GAIN WILD-TYPE  18  90 363  62
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 18
  T2               16                 90
  T3               54                363
  T4                5                 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
  11Q GAIN MUTATED    37  21  19
  11Q GAIN WILD-TYPE 308 129  96
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               37                308
  N1               21                129
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    51  17
  11Q GAIN WILD-TYPE 399  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     51   17
  11Q GAIN WILD-TYPE  399   71
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               51                399
  1               17                 71
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    36  41
  11Q GAIN WILD-TYPE 251 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     36   41
  11Q GAIN WILD-TYPE  251  284
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               36                251
  MALE                 41                284
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    56   3
  11Q GAIN WILD-TYPE 390  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     56    3
  11Q GAIN WILD-TYPE  390   25
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                56                390
  YES                3                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                     50                             1
  11Q GAIN WILD-TYPE                  332                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                      26                              0
  11Q GAIN WILD-TYPE                   120                             13
D22V10, multiclass
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         50                332
  COLON MUCINOUS ADENOCARCINOMA                 1                 59
  RECTAL ADENOCARCINOMA                        26                120
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    56   1   4   2
  11Q GAIN WILD-TYPE 386   4  33  27
D22V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               56                386
  R1                1                  4
  R2                4                 33
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          11    39
  11Q GAIN WILD-TYPE                        53   253
D22V13, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                      11                 53
  WHITE                                          39                253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  48
  11Q GAIN WILD-TYPE   4 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   48
  11Q GAIN WILD-TYPE    4  300
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                300
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    91  28
  12P GAIN WILD-TYPE 381  93
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               119                474 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                 93 
$`12P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
       15.62        12.66        44.91        13.94        37.02        14.53 
TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-A566 
       22.09        25.08        20.61        23.87        20.12        24.92 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        58.03         0.00        29.00        29.00        12.99 
TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       19.99        78.08         0.92        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 
        5.03        26.99        19.04        35.05         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3939 TCGA-AA-3941 
       14.93         0.00        33.07         0.00        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 
       26.01        24.00        18.05        12.00        31.00        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6963 
        0.92        22.03        39.98        40.96         0.07        27.42 
TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6607 
        0.92        18.84         5.13        49.41         6.77         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        1.61        12.69         3.06       148.01        85.45        15.62 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 
       20.02        25.02        32.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 
       14.04        11.01        20.19        17.75         4.80        14.30 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         4.80        12.00        10.26       119.70        24.43 
TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 
       44.32        95.18         8.61        47.87        44.68        13.78 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       74.79        10.98        15.65        34.49        37.74        16.83 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 
       10.39        36.03        46.03         2.01         6.05        19.99 
TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
       13.94         7.99        19.04         1.02        36.95         1.02 
TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 
       36.03        15.95        36.03        38.96        61.97        78.12 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 
        4.01         5.03         5.29       126.44        32.61        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
       18.28        17.69        13.64        11.97        18.28 

$`12P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       45.60        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       24.39        19.66        20.28        16.24        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       47.01        15.02        19.00        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 
       36.95        17.03        10.06         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       27.02        29.98        18.05        31.00         2.01        33.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K 
       34.98         1.02        15.02        10.98        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
        5.03        41.00        18.05        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
      106.75        22.36        65.00        62.79        88.21        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 
      100.01        29.56         5.23        11.74         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56        70.16        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       82.95         1.91       124.27        23.05        37.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
        3.68         4.41        12.43         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 
       35.97        60.79       117.07        98.24        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.04        35.80        26.17        91.79        46.75        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
       18.18        19.33        19.33         9.93        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        30.28        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        13.55        19.10        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       15.39        20.02        86.63        65.98        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        20.98         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       19.99        28.04        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X 
       64.01        10.98        51.98        49.97         1.94        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        12.39         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       19.99         5.95        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  0 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            148.01             140.38 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             18.28              20.73 
[1] "0.0 - 148.0 (18.3)" "0.0 - 140.4 (20.7)"
[1] "hr=" "1.3"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    94  33
  12P GAIN WILD-TYPE 352 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     94   33
  12P GAIN WILD-TYPE  352  129
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON                94                352
  RECTUM               33                129
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P GAIN MUTATED        19        1       11        45         1         1
  12P GAIN WILD-TYPE      85        0       25       128         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           4          3         10         13       11
  12P GAIN WILD-TYPE        22         15         73         41       52
                    vv
clus                 STAGE IVA STAGE IVB
  12P GAIN MUTATED           7         0
  12P GAIN WILD-TYPE        19         2
D23V4, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  19                 85
  STAGE IA                  1                  0
  STAGE II                 11                 25
  STAGE IIA                45                128
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 4                 22
  STAGE IIIA                3                 15
  STAGE IIIB               10                 73
  STAGE IIIC               13                 41
  STAGE IV                 11                 52
  STAGE IVA                 7                 19
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED     1  24  87  14
  12P GAIN WILD-TYPE  19  82 330  53
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                 19
  T2               24                 82
  T3               87                330
  T4               14                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P GAIN MUTATED    81  24  22
  12P GAIN WILD-TYPE 264 126  93
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               81                264
  N1               24                126
  N2               22                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    94  16
  12P GAIN WILD-TYPE 356  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     94   16
  12P GAIN WILD-TYPE  356   72
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               94                356
  1               16                 72
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    60  67
  12P GAIN WILD-TYPE 227 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     60   67
  12P GAIN WILD-TYPE  227  258
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               60                227
  MALE                 67                258
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    87   8
  12P GAIN WILD-TYPE 359  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     87    8
  12P GAIN WILD-TYPE  359   20
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                87                359
  YES                8                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                     80                            14
  12P GAIN WILD-TYPE                  302                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                      28                              4
  12P GAIN WILD-TYPE                   118                              9
D23V10, multiclass
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         80                302
  COLON MUCINOUS ADENOCARCINOMA                14                 46
  RECTAL ADENOCARCINOMA                        28                118
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    94   1   5   6
  12P GAIN WILD-TYPE 348   4  32  23
D23V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               94                348
  R1                1                  4
  R2                5                 32
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     3
  12P GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          11    57
  12P GAIN WILD-TYPE                        53   235
D23V13, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      11                 53
  WHITE                                          57                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  70
  12P GAIN WILD-TYPE   5 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   70
  12P GAIN WILD-TYPE    5  278
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               70                278
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    83  23
  12Q GAIN WILD-TYPE 389  98
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               106                487 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                 98 
$`12Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
       15.62        12.66        44.91        13.94        37.02        14.53 
TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-A566 
       22.09        25.08        20.61        23.87        20.12        24.92 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        58.03         0.00        29.00        29.00        12.99 
TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       19.99        78.08         0.92         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 
       26.99        19.04        35.05         0.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
        0.00        33.07         0.00        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I 
       24.00        26.01        18.05        18.05        12.00        31.00 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       51.98         0.92        22.03        39.98        40.96         0.07 
TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6608 TCGA-CA-5254 
        0.92        18.84        49.41         6.77         1.61        12.69 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4747 TCGA-CM-5860 
        3.06       148.01        85.45        15.62        25.02        32.02 
TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 
       15.02        21.99        13.02        14.04        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 
       17.75         4.80        14.30        11.64        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6703 
      119.70        24.43        44.32        95.18        35.74        47.87 
TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D 
       44.68        13.78        74.79        10.98        15.65        21.90 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3609 
       34.49        16.83        36.03        34.03         2.01        19.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A015 TCGA-AG-A02G 
       19.04         1.02         1.02        36.03        36.03        38.96 
TCGA-AG-A02N TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         4.01         5.03       126.44        32.61        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 
       18.28        17.69        13.64        11.97 

$`12Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       45.60        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       24.39        19.66        20.28        16.24        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01        15.02        11.01        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       38.99        36.95        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
        1.02        15.02        10.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       41.00        18.05        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56        70.16        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF 
        9.04         9.44         4.80         1.51        11.38        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       61.91        36.00        26.43        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        46.75        79.69        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        12.79        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        65.98        11.84        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03        34.03        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       14.01        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.95         5.29        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  0 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            148.01             140.38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.975             20.020 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    88  23
  12Q GAIN WILD-TYPE 358 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     88   23
  12Q GAIN WILD-TYPE  358  139
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON                88                358
  RECTUM               23                139
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q GAIN MUTATED        16        1        9        45         1         0
  12Q GAIN WILD-TYPE      88        0       27       128         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           3          4         10          9        6
  12Q GAIN WILD-TYPE        23         14         73         45       57
                    vv
clus                 STAGE IVA STAGE IVB
  12Q GAIN MUTATED           7         0
  12Q GAIN WILD-TYPE        19         2
D24V4, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  16                 88
  STAGE IA                  1                  0
  STAGE II                  9                 27
  STAGE IIA                45                128
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                4                 14
  STAGE IIIB               10                 73
  STAGE IIIC                9                 45
  STAGE IV                  6                 57
  STAGE IVA                 7                 19
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED     1  22  75  12
  12Q GAIN WILD-TYPE  19  84 342  55
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                 19
  T2               22                 84
  T3               75                342
  T4               12                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12Q GAIN MUTATED    75  25  11
  12Q GAIN WILD-TYPE 270 125 104
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               75                270
  N1               25                125
  N2               11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    86  12
  12Q GAIN WILD-TYPE 364  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     86   12
  12Q GAIN WILD-TYPE  364   76
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               86                364
  1               12                 76
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    56  55
  12Q GAIN WILD-TYPE 231 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     56   55
  12Q GAIN WILD-TYPE  231  270
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               56                231
  MALE                 55                270
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    80   4
  12Q GAIN WILD-TYPE 366  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     80    4
  12Q GAIN WILD-TYPE  366   24
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                80                366
  YES                4                 24
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                     73                            15
  12Q GAIN WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                      20                              2
  12Q GAIN WILD-TYPE                   126                             11
D24V10, multiclass
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         73                309
  COLON MUCINOUS ADENOCARCINOMA                15                 45
  RECTAL ADENOCARCINOMA                        20                126
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    85   1   4   4
  12Q GAIN WILD-TYPE 357   4  33  25
D24V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               85                357
  R1                1                  4
  R2                4                 33
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          12    47
  12Q GAIN WILD-TYPE                        52   245
D24V13, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                      12                 52
  WHITE                                          47                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"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  60
  12Q GAIN WILD-TYPE   5 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   60
  12Q GAIN WILD-TYPE    5  288
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               60                288
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   287  69
  13Q GAIN WILD-TYPE 185  52
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               356                237 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                69                 52 
$`13Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       46.65        43.76        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       13.94        16.57        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 
       32.91        30.44        29.19        33.53        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.16        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 
       61.84         9.63         5.03         7.04        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       58.03         6.97        38.99         9.07        24.03        36.03 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 
       14.01        33.99        21.01        13.02        24.00        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       19.99        13.94        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        15.02         5.98        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
       85.05        19.04        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       12.99        26.01        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       13.05        26.01        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W 
       13.94        19.00        34.03        38.04        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
        1.02        15.02        32.02        12.00        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       21.37         0.79         5.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       16.44        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 
       17.26        18.84       109.28        75.95         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 
        5.23        11.74         1.61        12.69         3.06         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4744 
       14.30        17.56       148.01        49.08         1.91        20.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       32.02         5.03        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        1.48         4.41        12.43        14.30         9.04         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        11.38        10.26       119.70       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 
       49.91        13.32         7.50       131.51         7.76         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       14.04        26.47       119.93        35.97        31.96         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       41.42        16.24        33.67         0.53        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 
       44.68        63.62        39.42        36.00        26.43        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       91.79        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       17.85        16.80        42.77        29.46        21.90        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       86.63        65.98        11.84         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 
        1.02        46.03        34.03        34.03         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
       13.94        19.99        20.98         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 
        1.02        17.03        46.03         6.02        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
       36.03         9.07        12.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97         1.94        38.96        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        0.72        26.43         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03         8.98        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       32.61         0.49        20.55        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
       32.19         0.66         0.69         0.76        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`13Q GAIN WILD-TYPE`
TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 
        1.61        43.43        42.90        24.33        37.05        37.25 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       37.02        31.63        22.09        22.06         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        56.25         3.02 
TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
        1.02        35.01        63.98         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3554 
       37.05         8.05        19.07         0.00        19.07        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       29.95        23.01        61.02         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        11.01        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       19.04        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3860 
        0.00         0.00        33.07         0.00        36.03        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       53.00        18.05        31.00        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
        2.01         2.01        21.99        34.06        25.02        24.00 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01K 
        0.99        17.03        21.99        34.98        10.98        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.06        51.98         5.03         0.92        22.03 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07        15.52        56.55         0.72        10.88 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.46         0.92        27.09        17.82        17.85        19.33 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94       106.75        88.21         6.77 
TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
      100.01         3.19         2.14         3.25         3.29        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.76        10.06        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
        9.99        21.14        82.95       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       25.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58         3.68         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64         1.51        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6302 
       47.87         1.55        34.42        13.25        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6321 
       53.62        55.04        85.48        35.93        61.91        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        26.17        79.69        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H 
        9.93        12.79        32.98         8.42        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       70.03        34.49        16.83        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        8.02        24.00        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        6.05        15.95         7.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A002 
       19.04         1.02        13.02        48.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       13.94        23.01        37.02         1.02        31.00        10.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00         1.45         1.81        10.19        33.17 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 
       13.97        15.02         5.95         5.29       126.44         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       19.96        20.91         8.61        13.64        17.46         8.45 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.53         1.12        12.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            148.01             140.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             19.99              20.42 
[1] "0.1 - 148.0 (20.0)" "0.0 - 140.4 (20.4)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   253 110
  13Q GAIN WILD-TYPE 193  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    253  110
  13Q GAIN WILD-TYPE  193   52
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON               253                193
  RECTUM              110                 52
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q GAIN MUTATED        60        0       18        87         4         3
  13Q GAIN WILD-TYPE      44        1       18        86         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED          16         15         55         37       48
  13Q GAIN WILD-TYPE        10          3         28         17       15
                    vv
clus                 STAGE IVA STAGE IVB
  13Q GAIN MUTATED          16         0
  13Q GAIN WILD-TYPE        10         2
D25V4, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  60                 44
  STAGE IA                  0                  1
  STAGE II                 18                 18
  STAGE IIA                87                 86
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                16                 10
  STAGE IIIA               15                  3
  STAGE IIIB               55                 28
  STAGE IIIC               37                 17
  STAGE IV                 48                 15
  STAGE IVA                16                 10
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    14  61 250  41
  13Q GAIN WILD-TYPE   6  45 167  26
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                  6
  T2               61                 45
  T3              250                167
  T4               41                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  13Q GAIN MUTATED   182 103  80
  13Q GAIN WILD-TYPE 163  47  35
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0              182                163
  N1              103                 47
  N2               80                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   262  62
  13Q GAIN WILD-TYPE 188  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    262   62
  13Q GAIN WILD-TYPE  188   26
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              262                188
  1               62                 26
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   166 201
  13Q GAIN WILD-TYPE 121 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    166  201
  13Q GAIN WILD-TYPE  121  124
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE              166                121
  MALE                201                124
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   270  21
  13Q GAIN WILD-TYPE 176   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    270   21
  13Q GAIN WILD-TYPE  176    7
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO               270                176
  YES               21                  7
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                    235                            17
  13Q GAIN WILD-TYPE                  147                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                     106                              3
  13Q GAIN WILD-TYPE                    40                             10
D25V10, multiclass
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        235                147
  COLON MUCINOUS ADENOCARCINOMA                17                 43
  RECTAL ADENOCARCINOMA                       106                 40
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   256   3  27  12
  13Q GAIN WILD-TYPE 186   2  10  17
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              256                186
  R1                3                  2
  R2               27                 10
  RX               12                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     4
  13Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                          38   189
  13Q GAIN WILD-TYPE                        26   103
D25V13, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      38                 26
  WHITE                                         189                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"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4 216
  13Q GAIN WILD-TYPE   1 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4  216
  13Q GAIN WILD-TYPE    1  132
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              216                132
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    36   6
  14Q GAIN WILD-TYPE 436 115
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                42                551 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                115 
$`14Q GAIN MUTATED`
TCGA-A6-2674 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6649 
       43.76        45.60        37.02        29.16        25.18        24.16 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3851 TCGA-AA-3852 
       26.01        12.99        20.98        78.08        33.07         0.00 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6890 
       24.00         2.01        19.00        10.98         0.92         0.79 
TCGA-AD-6965 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6719 TCGA-CM-5864 TCGA-CM-6678 
        0.20         3.19        12.69        14.30        15.02        11.01 
TCGA-D5-5539 TCGA-D5-6538 TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6307 
       19.59        17.13         6.12        95.18         1.55        55.04 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5YW TCGA-AF-6136 TCGA-AG-3611 
       46.75        74.79        12.79        29.46        15.39        13.94 
TCGA-AG-3999 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01Y TCGA-EI-6512 TCGA-EI-6885 
       28.04        15.95        12.00        64.01        17.69        13.64 

$`14Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       10.06         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
        0.72         5.79        22.42        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         1.61         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       65.85        53.62        44.68        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        91.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       10.98        19.33        19.33         9.93        15.65        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        42.77        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       30.28        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        16.83        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        19.99        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       19.99        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             95.18             148.01 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             17.41              20.02 
[1] "0.0 - 95.2 (17.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    35   8
  14Q GAIN WILD-TYPE 411 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     35    8
  14Q GAIN WILD-TYPE  411  154
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON                35                411
  RECTUM                8                154
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q GAIN MUTATED         6        0        3        11         0         0
  14Q GAIN WILD-TYPE      98        1       33       162        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          1          7          5        4
  14Q GAIN WILD-TYPE        26         17         76         49       59
                    vv
clus                 STAGE IVA STAGE IVB
  14Q GAIN MUTATED           3         1
  14Q GAIN WILD-TYPE        23         1
D26V4, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   6                 98
  STAGE IA                  0                  1
  STAGE II                  3                 33
  STAGE IIA                11                162
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                1                 17
  STAGE IIIB                7                 76
  STAGE IIIC                5                 49
  STAGE IV                  4                 59
  STAGE IVA                 3                 23
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     1   6  31   5
  14Q GAIN WILD-TYPE  19 100 386  62
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                 19
  T2                6                100
  T3               31                386
  T4                5                 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
  14Q GAIN MUTATED    22  11  10
  14Q GAIN WILD-TYPE 323 139 105
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               22                323
  N1               11                139
  N2               10                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    28   8
  14Q GAIN WILD-TYPE 422  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     28    8
  14Q GAIN WILD-TYPE  422   80
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               28                422
  1                8                 80
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    20  23
  14Q GAIN WILD-TYPE 267 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20   23
  14Q GAIN WILD-TYPE  267  302
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               20                267
  MALE                 23                302
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    30   1
  14Q GAIN WILD-TYPE 416  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     30    1
  14Q GAIN WILD-TYPE  416   27
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                30                416
  YES                1                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                     26                             9
  14Q GAIN WILD-TYPE                  356                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                       8                              0
  14Q GAIN WILD-TYPE                   138                             13
D26V10, multiclass
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         26                356
  COLON MUCINOUS ADENOCARCINOMA                 9                 51
  RECTAL ADENOCARCINOMA                         8                138
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    30   0   1   3
  14Q GAIN WILD-TYPE 412   5  36  26
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               30                412
  R1                0                  5
  R2                1                 36
  RX                3                 26
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  1     2
  14Q GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           2    22
  14Q GAIN WILD-TYPE                        62   270
D26V13, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                       2                 62
  WHITE                                          22                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"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  25
  14Q GAIN WILD-TYPE   5 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   25
  14Q GAIN WILD-TYPE    5  323
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               25                323
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    11   3
  15Q GAIN WILD-TYPE 461 118
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                579 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                118 
$`15Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-6649 TCGA-AA-3534 TCGA-AA-3941 TCGA-AZ-4614 TCGA-CA-5254 
       15.62        24.16        29.00        24.00         5.65        12.69 
TCGA-CM-6161 TCGA-D5-6531 TCGA-DM-A1DB TCGA-G4-6297 TCGA-AF-3400 TCGA-AG-A01W 
       15.02        17.75        44.32        82.39        34.49        70.03 
TCGA-EI-7004 TCGA-F5-6464 
        8.45         9.96 

$`15Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       35.31       133.18        28.21         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       30.28        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.65               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.39             148.01 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            20.875             19.990 
[1] "5.7 - 82.4 (20.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 435 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  435  158
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON                11                435
  RECTUM                4                158
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q GAIN MUTATED         2        0        1         5         0         0
  15Q GAIN WILD-TYPE     102        1       35       168        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           0          0          1          1        2
  15Q GAIN WILD-TYPE        26         18         82         53       61
                    vv
clus                 STAGE IVA STAGE IVB
  15Q GAIN MUTATED           3         0
  15Q GAIN WILD-TYPE        23         2
D27V4, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                102
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                 5                168
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                0                 18
  STAGE IIIB                1                 82
  STAGE IIIC                1                 53
  STAGE IV                  2                 61
  STAGE IVA                 3                 23
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     0   2   8   5
  15Q GAIN WILD-TYPE  20 104 409  62
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                 20
  T2                2                104
  T3                8                409
  T4                5                 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
  15Q GAIN MUTATED     8   3   4
  15Q GAIN WILD-TYPE 337 147 111
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                8                337
  N1                3                147
  N2                4                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 439  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  439   84
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               11                439
  1                4                 84
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 276 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  276  321
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                276
  MALE                  4                321
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   1
  15Q GAIN WILD-TYPE 435  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    1
  15Q GAIN WILD-TYPE  435   27
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                11                435
  YES                1                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                     10                             1
  15Q GAIN WILD-TYPE                  372                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                       2                              2
  15Q GAIN WILD-TYPE                   144                             11
D27V10, multiclass
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                372
  COLON MUCINOUS ADENOCARCINOMA                 1                 59
  RECTAL ADENOCARCINOMA                         2                144
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    11   0   1   1
  15Q GAIN WILD-TYPE 431   5  36  28
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               11                431
  R1                0                  5
  R2                1                 36
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           1     9
  15Q GAIN WILD-TYPE                        63   283
D27V13, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       1                 63
  WHITE                                           9                283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  11
  15Q GAIN WILD-TYPE   5 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   11
  15Q GAIN WILD-TYPE    5  337
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               11                337
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   120  21
  16P GAIN WILD-TYPE 352 100
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               141                452 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                100 
$`16P GAIN MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 
       39.45        43.76        43.43        24.33        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       45.60        16.57        37.25        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       29.16        24.13        23.87        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3673 
       33.99        13.02        24.00        19.99        19.99        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       47.01        15.02        19.00        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       17.03        33.07         0.99        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       29.98        12.99        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       16.08        26.01        27.02        34.03        42.02        15.02 
TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.00        33.04        40.96        22.42        27.42         0.20 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
        0.95        33.01        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 
       29.56         5.23         1.61        12.69         3.29        14.30 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
      148.01        49.08         9.99        20.02         8.02        13.02 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 
       22.98        32.02        17.03         2.96        29.03        14.99 
TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       15.02        10.06        19.59        18.25         1.32        15.12 
TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-F4-6460 TCGA-F4-6704 
       12.49         4.80        11.38        38.20        31.96         1.55 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       82.39        65.85        44.68        55.04        63.62        39.42 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D 
       26.43        13.78        46.75        15.65        12.79        21.90 
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       39.48        37.74        15.39        20.02        86.63        65.98 
TCGA-AG-3592 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3885 TCGA-AG-3890 
       34.03        13.94        20.98         7.99        17.95        17.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       19.99        36.03        46.03        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 
       12.00        31.00        38.96        38.04         0.72        10.19 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
        6.97         9.37        78.12        11.01         5.03         8.98 
TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
        5.03        24.13         0.49        17.69        16.31        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       28.57         0.39         0.76 

$`16P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 
       43.76        42.90        42.28        13.94        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        36.53        14.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
        0.00        19.07        34.03        29.00         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       21.01        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01         0.92        47.05        11.01         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       15.95        38.99         0.00        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3875 
       36.03        32.05        31.07        31.07        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       21.99        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       22.03        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
       15.52        56.55         0.79         0.72         5.79        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       23.05        37.02        25.02        26.04        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        16.04        21.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
        8.35        23.51        74.56        67.30        53.62        85.48 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       35.93        61.91        36.00        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        91.79        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N 
       34.49        10.39        14.50        16.83        10.39        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99        19.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.56         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        1.81         6.05        33.17         4.73        12.39         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       21.01        15.02        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        31.30        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.2                0.0 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            148.01             140.38 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             20.98              19.81 
[1] "0.2 - 148.0 (21.0)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   106  40
  16P GAIN WILD-TYPE 340 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    106   40
  16P GAIN WILD-TYPE  340  122
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON               106                340
  RECTUM               40                122
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P GAIN MUTATED        18        1        4        33         3         0
  16P GAIN WILD-TYPE      86        0       32       140         7         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           8          8         25         18       17
  16P GAIN WILD-TYPE        18         10         58         36       46
                    vv
clus                 STAGE IVA STAGE IVB
  16P GAIN MUTATED           6         1
  16P GAIN WILD-TYPE        20         1
D28V4, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  18                 86
  STAGE IA                  1                  0
  STAGE II                  4                 32
  STAGE IIA                33                140
  STAGE IIB                 3                  7
  STAGE IIC                 0                  3
  STAGE III                 8                 18
  STAGE IIIA                8                 10
  STAGE IIIB               25                 58
  STAGE IIIC               18                 36
  STAGE IV                 17                 46
  STAGE IVA                 6                 20
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED     5  25 100  16
  16P GAIN WILD-TYPE  15  81 317  51
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 15
  T2               25                 81
  T3              100                317
  T4               16                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16P GAIN MUTATED    65  46  35
  16P GAIN WILD-TYPE 280 104  80
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               65                280
  N1               46                104
  N2               35                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   100  24
  16P GAIN WILD-TYPE 350  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    100   24
  16P GAIN WILD-TYPE  350   64
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              100                350
  1               24                 64
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    70  77
  16P GAIN WILD-TYPE 217 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     70   77
  16P GAIN WILD-TYPE  217  248
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               70                217
  MALE                 77                248
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   112   8
  16P GAIN WILD-TYPE 334  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    112    8
  16P GAIN WILD-TYPE  334   20
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               112                334
  YES                8                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                    100                             5
  16P GAIN WILD-TYPE                  282                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                      40                              0
  16P GAIN WILD-TYPE                   106                             13
D28V10, multiclass
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        100                282
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                        40                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED   110   0  10   7
  16P GAIN WILD-TYPE 332   5  27  22
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0              110                332
  R1                0                  5
  R2               10                 27
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1     3
  16P GAIN WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          16    69
  16P GAIN WILD-TYPE                        48   223
D28V13, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      16                 48
  WHITE                                          69                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  81
  16P GAIN WILD-TYPE   4 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   81
  16P GAIN WILD-TYPE    4  267
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               81                267
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   118  22
  16Q GAIN WILD-TYPE 354  99
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               140                453 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                 99 
$`16Q GAIN MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 
       39.45        43.76        43.43        24.33        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 
       45.60        16.57        37.25        32.45        30.44        29.16 
TCGA-A6-6140 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       24.13        23.87        29.00        26.01        12.99        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       13.02        24.00        19.99        50.04        47.01        15.02 
TCGA-AA-3688 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 
       19.00        36.95        37.02        14.93        17.03        33.07 
TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3941 
        0.99        17.03        24.03        27.02        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-A00F 
       20.98        34.03        16.08        26.01        27.02        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 
       42.02        15.02        12.00        33.04        40.96        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK 
       27.42         0.20         0.95        33.01        17.26        18.84 
TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
        5.13        62.79        29.56         5.23         1.61        12.69 
TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 
        3.29       148.01        49.08         9.99        20.02         8.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        22.98        32.02        17.03         2.96        29.03 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 
       14.99        15.02        10.06        19.59        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 
       15.12        17.13        12.49         4.41         4.80        11.38 
TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 
       38.20        35.97         8.61        31.96         1.55        82.39 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 
       44.68        55.04        63.62        39.42        26.43        13.78 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 
       15.65        12.79        21.90        39.48        37.74        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3592 TCGA-AG-3611 
       15.39        20.02        86.63        65.98        34.03        13.94 
TCGA-AG-3725 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 
       20.98        17.95        17.03        19.99        36.03        46.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G 
       15.95        36.03         9.07        12.00        31.00        38.96 
TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 
       38.04         0.72        10.19         9.37        78.12        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.03         8.98         5.03        24.13        51.48         0.49 
TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       17.69        16.31        49.51        28.57         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6863 
        0.69         0.76 

$`16Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 
       43.76        42.90        42.28        13.94        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 
       19.07         0.00        19.07        34.03        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       14.01        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       54.02         2.01        14.01         0.92        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 
        0.00         0.00        36.03        32.05        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        29.98        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       26.01        24.00         2.01         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       13.05        34.06        25.02        24.00        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         5.79        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09        16.31        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65        32.94       106.75        22.36        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
       37.02        25.02        26.04        27.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       30.08        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        16.04        21.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       53.62        85.48        35.93        61.91        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       26.04        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       31.30        30.28        11.90        70.03        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        14.50        16.83 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       10.39        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
        1.02        48.03        32.02        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       23.01        37.02         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.97         1.94        61.97        41.00        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97         4.73        12.39         7.17        21.01        15.02 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
       31.30        32.19         0.53         1.12        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.2                0.0 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            148.01             140.38 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             20.50              19.99 
[1] "0.2 - 148.0 (20.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   103  41
  16Q GAIN WILD-TYPE 343 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    103   41
  16Q GAIN WILD-TYPE  343  121
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON               103                343
  RECTUM               41                121
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q GAIN MUTATED        17        1        4        32         2         0
  16Q GAIN WILD-TYPE      87        0       32       141         8         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           8          9         27         16       16
  16Q GAIN WILD-TYPE        18          9         56         38       47
                    vv
clus                 STAGE IVA STAGE IVB
  16Q GAIN MUTATED           7         1
  16Q GAIN WILD-TYPE        19         1
D29V4, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  1                  0
  STAGE II                  4                 32
  STAGE IIA                32                141
  STAGE IIB                 2                  8
  STAGE IIC                 0                  3
  STAGE III                 8                 18
  STAGE IIIA                9                  9
  STAGE IIIB               27                 56
  STAGE IIIC               16                 38
  STAGE IV                 16                 47
  STAGE IVA                 7                 19
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED     5  24 100  15
  16Q GAIN WILD-TYPE  15  82 317  52
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                5                 15
  T2               24                 82
  T3              100                317
  T4               15                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16Q GAIN MUTATED    62  48  34
  16Q GAIN WILD-TYPE 283 102  81
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               62                283
  N1               48                102
  N2               34                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    98  24
  16Q GAIN WILD-TYPE 352  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     98   24
  16Q GAIN WILD-TYPE  352   64
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               98                352
  1               24                 64
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    69  76
  16Q GAIN WILD-TYPE 218 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     69   76
  16Q GAIN WILD-TYPE  218  249
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               69                218
  MALE                 76                249
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   109   8
  16Q GAIN WILD-TYPE 337  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    109    8
  16Q GAIN WILD-TYPE  337   20
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO               109                337
  YES                8                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                     97                             5
  16Q GAIN WILD-TYPE                  285                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                      41                              0
  16Q GAIN WILD-TYPE                   105                             13
D29V10, multiclass
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         97                285
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                        41                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED   110   0   9   6
  16Q GAIN WILD-TYPE 332   5  28  23
D29V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0              110                332
  R1                0                  5
  R2                9                 28
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  1     2
  16Q GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          16    73
  16Q GAIN WILD-TYPE                        48   219
D29V13, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                      16                 48
  WHITE                                          73                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  84
  16Q GAIN WILD-TYPE   4 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   84
  16Q GAIN WILD-TYPE    4  264
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               84                264
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    36   2
  17P GAIN WILD-TYPE 436 119
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                555 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                119 
$`17P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 
       15.62         4.80        12.66        37.02        36.53        29.19 
TCGA-A6-6142 TCGA-A6-6652 TCGA-AA-3506 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 
       25.08        24.69        58.03        35.05         1.02        17.03 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-CA-6715 TCGA-CK-4948 
       12.99         2.01        13.05        34.06         0.07       148.01 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6929 
       22.03         2.96        11.01        15.12         4.80         4.80 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QG-A5YW TCGA-AG-3587 
       95.18         1.55        74.56        36.00        29.46        46.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6623 
       15.95        19.99        19.99         1.02        26.43         9.37 
TCGA-DC-6682 TCGA-G5-6641 
        4.01        26.43 

$`17P GAIN WILD-TYPE`
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.43        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       14.53        32.45        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13         8.38        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       50.99        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.61        12.69         3.06         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       85.48        63.62        39.42        35.93        61.91        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       42.77        32.98         8.42        31.30        21.90        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.81        10.19         6.05        33.17         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            148.01             140.38 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.51              20.02 
[1] "0.1 - 148.0 (18.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.8"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29   9
  17P GAIN WILD-TYPE 417 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    9
  17P GAIN WILD-TYPE  417  153
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON                29                417
  RECTUM                9                153
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P GAIN MUTATED         9        0        0        10         0         0
  17P GAIN WILD-TYPE      95        1       36       163        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1          1          5          6        3
  17P GAIN WILD-TYPE        25         17         78         48       60
                    vv
clus                 STAGE IVA STAGE IVB
  17P GAIN MUTATED           3         0
  17P GAIN WILD-TYPE        23         2
D30V4, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   9                 95
  STAGE IA                  0                  1
  STAGE II                  0                 36
  STAGE IIA                10                163
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                1                 17
  STAGE IIIB                5                 78
  STAGE IIIC                6                 48
  STAGE IV                  3                 60
  STAGE IVA                 3                 23
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     3   7  24   4
  17P GAIN WILD-TYPE  17  99 393  63
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                3                 17
  T2                7                 99
  T3               24                393
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17P GAIN MUTATED    20  11   7
  17P GAIN WILD-TYPE 325 139 108
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               20                325
  N1               11                139
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    25   6
  17P GAIN WILD-TYPE 425  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     25    6
  17P GAIN WILD-TYPE  425   82
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               25                425
  1                6                 82
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    18  20
  17P GAIN WILD-TYPE 269 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18   20
  17P GAIN WILD-TYPE  269  305
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               18                269
  MALE                 20                305
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29   1
  17P GAIN WILD-TYPE 417  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    1
  17P GAIN WILD-TYPE  417   27
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                29                417
  YES                1                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                     24                             5
  17P GAIN WILD-TYPE                  358                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                       8                              1
  17P GAIN WILD-TYPE                   138                             12
D30V10, multiclass
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         24                358
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                         8                138
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    28   0   2   2
  17P GAIN WILD-TYPE 414   5  35  27
D30V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               28                414
  R1                0                  5
  R2                2                 35
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  1     1
  17P GAIN WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           6    17
  17P GAIN WILD-TYPE                        58   275
D30V13, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       6                 58
  WHITE                                          17                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"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  24
  17P GAIN WILD-TYPE   4 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   24
  17P GAIN WILD-TYPE    4  324
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               24                324
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    90  15
  17Q GAIN WILD-TYPE 382 106
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               105                488 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                106 
$`17Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-2677 
       15.62        12.66         1.61        39.45        43.43        24.33 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       37.02        36.53        14.53        30.44        29.19        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3494 TCGA-AA-3496 
       27.09        25.08        25.18        24.69         1.02         1.02 
TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3692 TCGA-AA-3812 TCGA-AA-3821 
       58.03        24.00        23.01        36.00        35.05         1.02 
TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 
       17.03         0.99        24.03        12.99        34.03         2.01 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G 
       50.99        13.05        34.06        38.04        21.99        12.00 
TCGA-AA-A01S TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 
        1.02        15.52         0.79        27.42        16.44        16.31 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 
       88.21        29.56         3.19         0.07       148.01         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       29.06        22.03        17.03         2.96        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 
       14.99        13.05        11.08        11.01        19.59        55.92 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A1D0 
        1.32        15.12         4.80        17.13         4.80       130.65 
TCGA-DM-A285 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        6.12        95.18        74.56        65.85        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6626 TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2690 
       39.42        36.00        46.75        29.46        30.28        17.23 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 
       86.63        11.84        12.00        46.03        34.03        15.95 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       19.99        19.99        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 
        9.07        31.00         0.69        26.43         6.05         8.98 
TCGA-DC-6682 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
        4.01        51.48        17.00        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6641 
       32.19        12.46        26.43 

$`17Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         9.53        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        34.65        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        32.71        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       24.13         8.38        24.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       37.05        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
        0.99        25.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       21.99        16.08        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37        56.55         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       15.02        12.00        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6314 
       23.51        67.30        53.62        44.68        85.48        35.93 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       61.91        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        91.79        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        42.77        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 
       15.39        20.02        10.39        65.98        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02        36.03         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         1.81        10.19        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02         5.03        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        19.96        20.91        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            148.01             140.38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.99              19.99 
[1] "0.1 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    80  30
  17Q GAIN WILD-TYPE 366 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     80   30
  17Q GAIN WILD-TYPE  366  132
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON                80                366
  RECTUM               30                132
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q GAIN MUTATED        16        0        3        29         0         0
  17Q GAIN WILD-TYPE      88        1       33       144        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           4          4         15         11       16
  17Q GAIN WILD-TYPE        22         14         68         43       47
                    vv
clus                 STAGE IVA STAGE IVB
  17Q GAIN MUTATED           8         1
  17Q GAIN WILD-TYPE        18         1
D31V4, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  16                 88
  STAGE IA                  0                  1
  STAGE II                  3                 33
  STAGE IIA                29                144
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 4                 22
  STAGE IIIA                4                 14
  STAGE IIIB               15                 68
  STAGE IIIC               11                 43
  STAGE IV                 16                 47
  STAGE IVA                 8                 18
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED     5  18  78   9
  17Q GAIN WILD-TYPE  15  88 339  58
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                 15
  T2               18                 88
  T3               78                339
  T4                9                 58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17Q GAIN MUTATED    57  30  23
  17Q GAIN WILD-TYPE 288 120  92
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               57                288
  N1               30                120
  N2               23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    70  24
  17Q GAIN WILD-TYPE 380  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     70   24
  17Q GAIN WILD-TYPE  380   64
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               70                380
  1               24                 64
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    51  59
  17Q GAIN WILD-TYPE 236 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51   59
  17Q GAIN WILD-TYPE  236  266
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               51                236
  MALE                 59                266
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    81   5
  17Q GAIN WILD-TYPE 365  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     81    5
  17Q GAIN WILD-TYPE  365   23
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                81                365
  YES                5                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                     71                             8
  17Q GAIN WILD-TYPE                  311                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                      29                              1
  17Q GAIN WILD-TYPE                   117                             12
D31V10, multiclass
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         71                311
  COLON MUCINOUS ADENOCARCINOMA                 8                 52
  RECTAL ADENOCARCINOMA                        29                117
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    78   1  10   2
  17Q GAIN WILD-TYPE 364   4  27  27
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               78                364
  R1                1                  4
  R2               10                 27
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          14    58
  17Q GAIN WILD-TYPE                        50   234
D31V13, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                      14                 50
  WHITE                                          58                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"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3  67
  17Q GAIN WILD-TYPE   2 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   67
  17Q GAIN WILD-TYPE    2  281
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               67                281
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    22   8
  18P GAIN WILD-TYPE 450 113
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                30                563 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                113 
$`18P GAIN MUTATED`
TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-A01D 
       24.16        24.39        54.02         5.98        10.06        10.98 
TCGA-AA-A01Z TCGA-AD-5900 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6171 TCGA-CM-6675 
       37.02         0.07         3.19        27.02        14.04        13.05 
TCGA-CM-6676 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 TCGA-DM-A1DA 
       11.08        17.75        16.14         4.41        11.64         7.50 
TCGA-DM-A285 TCGA-DM-A28K TCGA-G4-6299 TCGA-NH-A50V TCGA-NH-A6GA TCGA-AF-6672 
        6.12        98.24        74.56        19.33         9.93        10.39 
TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-A01Y TCGA-AG-A02G TCGA-DT-5265 TCGA-F5-6464 
       32.02         6.05        64.01        38.96         5.29         9.96 

$`18P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       12.99        13.02        15.02        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        15.65        12.79        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        15.39        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       70.03        10.98        51.98        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.24             148.01 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            12.345             20.120 
[1] "0.1 - 98.2 (12.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25   8
  18P GAIN WILD-TYPE 421 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25    8
  18P GAIN WILD-TYPE  421  154
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON                25                421
  RECTUM                8                154
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P GAIN MUTATED         5        0        5         4         0         0
  18P GAIN WILD-TYPE      99        1       31       169        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           3          1          3          7        4
  18P GAIN WILD-TYPE        23         17         80         47       59
                    vv
clus                 STAGE IVA STAGE IVB
  18P GAIN MUTATED           0         1
  18P GAIN WILD-TYPE        26         1
D32V4, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   5                 99
  STAGE IA                  0                  1
  STAGE II                  5                 31
  STAGE IIA                 4                169
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                1                 17
  STAGE IIIB                3                 80
  STAGE IIIC                7                 47
  STAGE IV                  4                 59
  STAGE IVA                 0                 26
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   6  22   5
  18P GAIN WILD-TYPE  20 100 395  62
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                 20
  T2                6                100
  T3               22                395
  T4                5                 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
  18P GAIN MUTATED    14   6  13
  18P GAIN WILD-TYPE 331 144 102
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               14                331
  N1                6                144
  N2               13                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24   4
  18P GAIN WILD-TYPE 426  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24    4
  18P GAIN WILD-TYPE  426   84
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               24                426
  1                4                 84
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    11  22
  18P GAIN WILD-TYPE 276 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11   22
  18P GAIN WILD-TYPE  276  303
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                276
  MALE                 22                303
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    22   2
  18P GAIN WILD-TYPE 424  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22    2
  18P GAIN WILD-TYPE  424   26
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                22                424
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                     18                             7
  18P GAIN WILD-TYPE                  364                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                       6                              2
  18P GAIN WILD-TYPE                   140                             11
D32V10, multiclass
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         18                364
  COLON MUCINOUS ADENOCARCINOMA                 7                 53
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    23   0   1   1
  18P GAIN WILD-TYPE 419   5  36  28
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               23                419
  R1                0                  5
  R2                1                 36
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     1
  18P GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           3    19
  18P GAIN WILD-TYPE                        61   273
D32V13, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       3                 61
  WHITE                                          19                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  23
  18P GAIN WILD-TYPE   5 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   23
  18P GAIN WILD-TYPE    5  325
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               23                325
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    13   3
  18Q GAIN WILD-TYPE 459 118
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                577 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                118 
$`18Q GAIN MUTATED`
TCGA-A6-6653 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AD-5900 TCGA-AZ-6607 
       24.39        54.02         5.98        10.06         0.07         3.19 
TCGA-CM-6171 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 TCGA-DM-A28K 
       14.04        17.75        16.14         4.41        11.64        98.24 
TCGA-G4-6299 TCGA-AF-6672 TCGA-DT-5265 TCGA-F5-6464 
       74.56        10.39         5.29         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M 
       81.37       119.93        35.97        60.79       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        23.51        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        30.28        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.24             148.01 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            11.015             20.050 
[1] "0.1 - 98.2 (11.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    15   4
  18Q GAIN WILD-TYPE 431 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     15    4
  18Q GAIN WILD-TYPE  431  158
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON                15                431
  RECTUM                4                158
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q GAIN MUTATED         4        0        3         3         0         0
  18Q GAIN WILD-TYPE     100        1       33       170        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           3          1          0          3        2
  18Q GAIN WILD-TYPE        23         17         83         51       61
                    vv
clus                 STAGE IVA STAGE IVB
  18Q GAIN MUTATED           0         0
  18Q GAIN WILD-TYPE        26         2
D33V4, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   4                100
  STAGE IA                  0                  1
  STAGE II                  3                 33
  STAGE IIA                 3                170
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                1                 17
  STAGE IIIB                0                 83
  STAGE IIIC                3                 51
  STAGE IV                  2                 61
  STAGE IVA                 0                 26
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   4  11   4
  18Q GAIN WILD-TYPE  20 102 406  63
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                 20
  T2                4                102
  T3               11                406
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18Q GAIN MUTATED    10   3   6
  18Q GAIN WILD-TYPE 335 147 109
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               10                335
  N1                3                147
  N2                6                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    14   1
  18Q GAIN WILD-TYPE 436  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     14    1
  18Q GAIN WILD-TYPE  436   87
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               14                436
  1                1                 87
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  13
  18Q GAIN WILD-TYPE 281 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   13
  18Q GAIN WILD-TYPE  281  312
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                281
  MALE                 13                312
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    12   1
  18Q GAIN WILD-TYPE 434  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12    1
  18Q GAIN WILD-TYPE  434   27
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                434
  YES                1                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                     10                             5
  18Q GAIN WILD-TYPE                  372                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                       3                              1
  18Q GAIN WILD-TYPE                   143                             12
D33V10, multiclass
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                372
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                         3                143
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    13   0   0   1
  18Q GAIN WILD-TYPE 429   5  37  28
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               13                429
  R1                0                  5
  R2                0                 37
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     1
  18Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0    14
  18Q GAIN WILD-TYPE                        64   278
D33V13, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       0                 64
  WHITE                                          14                278
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  15
  18Q GAIN WILD-TYPE   5 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   15
  18Q GAIN WILD-TYPE    5  333
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               15                333
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    82  17
  19P GAIN WILD-TYPE 390 104
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                99                494 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                104 
$`19P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
       15.62        12.66        43.76        43.43        45.60        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       37.02        36.53        14.53        31.63        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 
       21.76        23.87        56.25        37.05        35.05         0.99 
TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00K 
       31.07        50.99        13.05        27.02        13.94        18.05 
TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 
       42.02        21.99        51.98         0.92         5.79        22.42 
TCGA-AD-A5EK TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 
       16.44        18.84        88.21        29.56        11.74         3.06 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 
       14.30        85.45         9.99         1.91        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 
       29.06        32.02         5.03        15.02        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 
       29.03        21.99        13.02        11.08        19.59        56.09 
TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6297 
       15.12        11.38       119.70        35.97         8.61        82.39 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 
       74.56        63.62        39.42        26.43        74.79        17.85 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L 
       29.46        21.90        39.48        17.23        86.63        65.98 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 
       36.03        46.03        34.03        34.03         6.05        19.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 
        0.99        19.99         1.02        36.03         1.02        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-DC-4745 
       12.00        31.00         1.94        38.04         6.05        21.01 
TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 
       11.01         8.98        27.95         4.01       129.27        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6863 
       17.69        16.31         0.76 

$`19P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
        4.80         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
       42.90        24.33        42.28        44.91        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.05        37.25        34.65        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       16.08        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07         7.96        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         2.01         5.03        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13       106.75        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         2.14         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
       12.76        10.06        17.56       148.01        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        12.00        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21         8.35        23.51        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        35.93        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30        30.28        11.90        70.03        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       14.50        16.83        15.39        20.02        10.39        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       14.01        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        4.73        12.39        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        15.02        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.76               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             148.01 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            21.900             19.975 
[1] "0.8 - 129.3 (21.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    72  32
  19P GAIN WILD-TYPE 374 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     72   32
  19P GAIN WILD-TYPE  374  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON                72                374
  RECTUM               32                130
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P GAIN MUTATED        17        0        5        31         0         0
  19P GAIN WILD-TYPE      87        1       31       142        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           4          2         19          7       12
  19P GAIN WILD-TYPE        22         16         64         47       51
                    vv
clus                 STAGE IVA STAGE IVB
  19P GAIN MUTATED           5         0
  19P GAIN WILD-TYPE        21         2
D34V4, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  0                  1
  STAGE II                  5                 31
  STAGE IIA                31                142
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 4                 22
  STAGE IIIA                2                 16
  STAGE IIIB               19                 64
  STAGE IIIC                7                 47
  STAGE IV                 12                 51
  STAGE IVA                 5                 21
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED     2  18  74  10
  19P GAIN WILD-TYPE  18  88 343  57
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                2                 18
  T2               18                 88
  T3               74                343
  T4               10                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19P GAIN MUTATED    57  31  16
  19P GAIN WILD-TYPE 288 119  99
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               57                288
  N1               31                119
  N2               16                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    70  17
  19P GAIN WILD-TYPE 380  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     70   17
  19P GAIN WILD-TYPE  380   71
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               70                380
  1               17                 71
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    44  60
  19P GAIN WILD-TYPE 243 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     44   60
  19P GAIN WILD-TYPE  243  265
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               44                243
  MALE                 60                265
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    74   7
  19P GAIN WILD-TYPE 372  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     74    7
  19P GAIN WILD-TYPE  372   21
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                74                372
  YES                7                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                     65                             7
  19P GAIN WILD-TYPE                  317                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                      32                              0
  19P GAIN WILD-TYPE                   114                             13
D34V10, multiclass
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         65                317
  COLON MUCINOUS ADENOCARCINOMA                 7                 53
  RECTAL ADENOCARCINOMA                        32                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    75   2   5   7
  19P GAIN WILD-TYPE 367   3  32  22
D34V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               75                367
  R1                2                  3
  R2                5                 32
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                          15    55
  19P GAIN WILD-TYPE                        49   237
D34V13, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                      15                 49
  WHITE                                          55                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  68
  19P GAIN WILD-TYPE   5 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   68
  19P GAIN WILD-TYPE    5  280
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               68                280
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    89  18
  19Q GAIN WILD-TYPE 383 103
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               107                486 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                103 
$`19Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 
       15.62        12.66        39.45        43.76        43.43        45.60 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 
       16.57        37.02        36.53        14.53        31.63        29.16 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       25.08        25.18        21.76        23.87        61.84        56.25 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3529 TCGA-AA-3542 TCGA-AA-3812 TCGA-AA-3818 
       35.01        58.03         0.00        12.99        35.05         0.99 
TCGA-AA-3854 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O 
       36.03        12.99        50.99        13.05        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 
       42.02        12.00        51.98         0.92         5.79        22.42 
TCGA-AD-A5EK TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
       16.44        17.85        18.84        88.21        29.56        11.74 
TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
        3.06        14.30        85.45         9.99         1.91        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       25.02        13.02        29.06        32.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 
       15.02         2.96        29.03        21.99        11.08        19.59 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       15.12         4.80        11.64        12.00        11.38       119.70 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6310 
       35.97         8.61        35.74        47.41        82.39        63.62 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QL-A97D 
       39.42        26.43        74.79        17.85        29.46        21.90 
TCGA-AF-2689 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3609 
       39.48        86.63        65.98        46.03        34.03        19.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 
        0.99        19.99         1.02         1.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 
        9.07        12.00        31.00         1.94        38.04         6.05 
TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       12.39        11.01         8.98        27.95         4.01       129.27 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       20.55        17.69        16.31        13.64         0.76 

$`19Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
       24.33        42.28        44.91        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       37.25        34.65        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       22.52        24.13         8.38        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        38.04         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         2.01         5.03        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       33.01        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        65.00        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01         5.23         3.19         1.61        12.69 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        27.02        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        17.03        12.00        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.26        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25         1.32        43.27        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 
       14.30         9.04         9.44         4.80         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
      119.93        60.79       117.07        98.24        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      133.18        28.21         8.35        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       65.85        53.62        44.68        55.04        85.48        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       61.91        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        91.79        46.75        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       42.77        32.98         8.42        31.30        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        10.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W 
        6.02        25.97        23.01        37.02         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19        33.17         6.97         9.37         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       78.12         7.17        21.01        15.02         5.03        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.02        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12        12.46        18.28        55.76        47.08        26.43 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             148.01 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             20.55              19.99 
[1] "0.0 - 129.3 (20.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    82  32
  19Q GAIN WILD-TYPE 364 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     82   32
  19Q GAIN WILD-TYPE  364  130
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON                82                364
  RECTUM               32                130
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q GAIN MUTATED        21        0        4        33         0         0
  19Q GAIN WILD-TYPE      83        1       32       140        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           3          3         19          9       14
  19Q GAIN WILD-TYPE        23         15         64         45       49
                    vv
clus                 STAGE IVA STAGE IVB
  19Q GAIN MUTATED           6         0
  19Q GAIN WILD-TYPE        20         2
D35V4, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  21                 83
  STAGE IA                  0                  1
  STAGE II                  4                 32
  STAGE IIA                33                140
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                3                 15
  STAGE IIIB               19                 64
  STAGE IIIC                9                 45
  STAGE IV                 14                 49
  STAGE IVA                 6                 20
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED     3  21  78  12
  19Q GAIN WILD-TYPE  17  85 339  55
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 17
  T2               21                 85
  T3               78                339
  T4               12                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19Q GAIN MUTATED    62  34  18
  19Q GAIN WILD-TYPE 283 116  97
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               62                283
  N1               34                116
  N2               18                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    75  20
  19Q GAIN WILD-TYPE 375  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     75   20
  19Q GAIN WILD-TYPE  375   68
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               75                375
  1               20                 68
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    50  64
  19Q GAIN WILD-TYPE 237 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     50   64
  19Q GAIN WILD-TYPE  237  261
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               50                237
  MALE                 64                261
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    83   5
  19Q GAIN WILD-TYPE 363  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     83    5
  19Q GAIN WILD-TYPE  363   23
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                83                363
  YES                5                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                     71                            11
  19Q GAIN WILD-TYPE                  311                            49
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                      32                              0
  19Q GAIN WILD-TYPE                   114                             13
D35V10, multiclass
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         71                311
  COLON MUCINOUS ADENOCARCINOMA                11                 49
  RECTAL ADENOCARCINOMA                        32                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    81   2   6   7
  19Q GAIN WILD-TYPE 361   3  31  22
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               81                361
  R1                2                  3
  R2                6                 31
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     2
  19Q GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          18    59
  19Q GAIN WILD-TYPE                        46   233
D35V13, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                      18                 46
  WHITE                                          59                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"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  73
  19Q GAIN WILD-TYPE   3 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   73
  19Q GAIN WILD-TYPE    3  275
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               73                275
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   269  71
  20P GAIN WILD-TYPE 203  50
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               340                253 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                71                 50 
$`20P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       15.62         4.80        39.45        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6142 
       32.91        30.44        29.19        23.61        27.09        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3529 
        1.02        58.03         6.97         1.02        36.03         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       19.07        34.03        29.00        29.00        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       21.01        13.02        23.01        20.98        13.94        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       35.05         0.99        25.02        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
        0.00        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       31.07        17.03        27.02        18.05        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       26.01        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       18.05        38.04         4.01        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        0.92        41.00        39.98         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        0.79         0.72         5.79        22.42        27.42        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
        0.46        14.50        16.31         0.95        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       17.85        19.33        18.84         1.41         5.13       106.75 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.07        14.30        17.56       148.01        85.45        49.08 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        25.02         8.02        13.02        29.06        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        13.02        14.04        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        45.40        12.26        19.59 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       20.19        17.75         1.32        17.85        12.49         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
        3.68         4.41         9.04        11.64         4.80        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E 
       12.59         7.50       139.17         6.12        14.04       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        95.18         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 
        6.18         1.55        41.42        33.67        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       28.21        82.39        55.04        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.04        13.78        91.79        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       18.18        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 
       32.98        21.90        24.13        39.48        17.23        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       37.74        10.39        16.83        20.02        10.39        65.98 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
       15.95        19.99        13.94        19.99        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        37.02         0.99         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       17.03        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X 
       23.01        37.02        36.03         9.07        51.98        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       12.39        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36       129.27        24.13        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.31        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       49.51         0.39        32.19         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

$`20P GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       12.66         1.61         9.53        46.65        42.90        42.28 
TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       37.05        31.63        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 
       29.16        22.52        24.13         8.38        20.61        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        56.25         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3543 
       24.03        37.05         8.05        19.07        26.01         0.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3655 
       33.99        24.00        17.95        29.95        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 
       78.08         6.97        54.02         0.92        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
        5.98        26.99        19.04        19.04         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        24.03        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 
       26.01        24.00         2.01         2.01        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01P 
       27.02        42.02         0.99        34.98         1.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6964 
       39.98        22.03        18.05        40.96        56.55        10.88 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 
        0.20         0.92        27.09        21.44        17.82       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
       75.95        58.39         5.65        32.94        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        6.77       100.01        11.74         3.25        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       10.06        70.16        15.62        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       82.95         1.91       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 
       27.02        22.03        30.08        32.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6679 
       29.03        12.99        15.02        12.95        13.05        10.06 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       12.03        56.09        55.92        20.42        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 
       15.12         4.80        17.13        16.14        15.58        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 
       14.30         9.44         1.51        12.00        92.75        49.91 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A 
      140.38        44.32       131.51       135.65         7.76        26.47 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       81.37        60.79        98.24        11.11        35.74        47.87 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 
       34.42        16.24        13.25         0.53        35.31         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       85.48        36.00        26.43        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 
       79.69        10.98        19.33        19.33         9.93        17.85 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 
        8.42        31.30        30.28        11.90        70.03        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N 
       13.55        34.49        14.50        15.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 
       36.03        12.00        32.02         2.01         6.05         0.99 
TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 
        7.99        32.98        19.04        19.99        17.95        13.02 
TCGA-AG-3893 TCGA-AG-3902 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       35.01        32.02         3.98        46.03        20.98        13.94 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 
       10.98        49.97         1.94        38.96        61.97        33.17 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD 
       78.12         7.17         4.01         5.03         5.29        57.24 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       51.48         0.49        19.96        16.34        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       17.46         8.45        31.30        28.57         0.69        12.46 
TCGA-G5-6641 
       26.43 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            148.01             140.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             18.28              22.36 
[1] "0.0 - 148.0 (18.3)" "0.0 - 140.4 (22.4)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   242 106
  20P GAIN WILD-TYPE 204  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    242  106
  20P GAIN WILD-TYPE  204   56
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON               242                204
  RECTUM              106                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P GAIN MUTATED        63        1       13        87         4         2
  20P GAIN WILD-TYPE      41        0       23        86         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          14         15         44         32       47
  20P GAIN WILD-TYPE        12          3         39         22       16
                    vv
clus                 STAGE IVA STAGE IVB
  20P GAIN MUTATED          17         1
  20P GAIN WILD-TYPE         9         1
D36V4, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  63                 41
  STAGE IA                  1                  0
  STAGE II                 13                 23
  STAGE IIA                87                 86
  STAGE IIB                 4                  6
  STAGE IIC                 2                  1
  STAGE III                14                 12
  STAGE IIIA               15                  3
  STAGE IIIB               44                 39
  STAGE IIIC               32                 22
  STAGE IV                 47                 16
  STAGE IVA                17                  9
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED    12  66 235  35
  20P GAIN WILD-TYPE   8  40 182  32
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               12                  8
  T2               66                 40
  T3              235                182
  T4               35                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20P GAIN MUTATED   182  92  74
  20P GAIN WILD-TYPE 163  58  41
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              182                163
  N1               92                 58
  N2               74                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   247  64
  20P GAIN WILD-TYPE 203  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    247   64
  20P GAIN WILD-TYPE  203   24
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              247                203
  1               64                 24
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   156 194
  20P GAIN WILD-TYPE 131 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    156  194
  20P GAIN WILD-TYPE  131  131
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              156                131
  MALE                194                131
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   249  19
  20P GAIN WILD-TYPE 197   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    249   19
  20P GAIN WILD-TYPE  197    9
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               249                197
  YES               19                  9
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                    220                            19
  20P GAIN WILD-TYPE                  162                            41
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                     100                              4
  20P GAIN WILD-TYPE                    46                              9
D36V10, multiclass
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        220                162
  COLON MUCINOUS ADENOCARCINOMA                19                 41
  RECTAL ADENOCARCINOMA                       100                 46
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   248   3  25  11
  20P GAIN WILD-TYPE 194   2  12  18
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              248                194
  R1                3                  2
  R2               25                 12
  RX               11                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     6
  20P GAIN WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          34   172
  20P GAIN WILD-TYPE                        30   120
D36V13, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      34                 30
  WHITE                                         172                120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 198
  20P GAIN WILD-TYPE   3 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  198
  20P GAIN WILD-TYPE    3  150
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              198                150
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   360  87
  20Q GAIN WILD-TYPE 112  34
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               447                146 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                87                 34 
$`20Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.45        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.16        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05         1.02        58.03         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
        9.07        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.05        47.01        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        85.05        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
       31.07        17.03        24.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       19.07         7.96        13.94        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.46        14.50        16.31         0.95        33.01 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
       17.26        17.85        19.33        18.84       109.28         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13       106.75        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       17.56       148.01        85.45        49.08         9.99         1.91 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        25.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         4.80        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
       38.20       130.65        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       44.32       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       35.97       117.07        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        47.41       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        8.35        82.39        23.51        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       26.43        26.04        13.78        91.79        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       18.18        15.65        12.79        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       29.46        32.98         8.42        21.90        30.28        11.90 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       24.13        39.48        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       86.63        65.98        11.84        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        46.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
       33.17         6.97         9.37         4.73        12.39         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`20Q GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       12.66         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       31.63        33.53        22.09        22.06         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       63.98        13.02         1.02        24.03        37.05         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
        0.99        17.95        29.95        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        0.92        11.01         5.98        26.99        19.04        19.04 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        1.02        17.98        15.95         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        27.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       18.05         0.99        34.98        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
       35.01        39.06        22.03        18.05        56.55        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
        0.92        27.09        21.44        17.82        75.95        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
        5.65        32.94        88.21         6.77       100.01        11.74 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        3.25        12.76        10.06        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 
       21.14        82.95       124.27        23.05        26.04        27.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       15.02        12.00        12.99        12.95        13.05        12.03 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 
       20.42        43.27        16.14        15.58         9.44         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.00        92.75       140.38       131.51       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 
       81.37        60.79        98.24        11.11        47.87        35.31 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       67.30        53.62        85.48        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       79.69        10.98        19.33        19.33         9.93        31.30 
TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 
       70.03        13.55        34.49        12.00        32.02         2.01 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 
        6.05        32.98        19.04        13.02         3.98        20.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-CL-5917 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
       49.97        61.97        78.12         5.29        19.96         8.61 
TCGA-EI-6917 TCGA-EI-7004 
       17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            148.01             140.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            19.590             22.045 
[1] "0.0 - 148.0 (19.6)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   315 144
  20Q GAIN WILD-TYPE 131  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    315  144
  20Q GAIN WILD-TYPE  131   18
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON               315                131
  RECTUM              144                 18
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q GAIN MUTATED        79        1       21       117         5         3
  20Q GAIN WILD-TYPE      25        0       15        56         5         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          19         17         66         43       56
  20Q GAIN WILD-TYPE         7          1         17         11        7
                    vv
clus                 STAGE IVA STAGE IVB
  20Q GAIN MUTATED          23         1
  20Q GAIN WILD-TYPE         3         1
D37V4, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  79                 25
  STAGE IA                  1                  0
  STAGE II                 21                 15
  STAGE IIA               117                 56
  STAGE IIB                 5                  5
  STAGE IIC                 3                  0
  STAGE III                19                  7
  STAGE IIIA               17                  1
  STAGE IIIB               66                 17
  STAGE IIIC               43                 11
  STAGE IV                 56                  7
  STAGE IVA                23                  3
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED    14  85 316  45
  20Q GAIN WILD-TYPE   6  21 101  22
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               14                  6
  T2               85                 21
  T3              316                101
  T4               45                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20Q GAIN MUTATED   241 128  91
  20Q GAIN WILD-TYPE 104  22  24
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              241                104
  N1              128                 22
  N2               91                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   329  78
  20Q GAIN WILD-TYPE 121  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    329   78
  20Q GAIN WILD-TYPE  121   10
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              329                121
  1               78                 10
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   210 252
  20Q GAIN WILD-TYPE  77  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    210  252
  20Q GAIN WILD-TYPE   77   73
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              210                 77
  MALE                252                 73
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   329  24
  20Q GAIN WILD-TYPE 117   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    329   24
  20Q GAIN WILD-TYPE  117    4
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               329                117
  YES               24                  4
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                    288                            24
  20Q GAIN WILD-TYPE                   94                            36
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                     135                              7
  20Q GAIN WILD-TYPE                    11                              6
D37V10, multiclass
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        288                 94
  COLON MUCINOUS ADENOCARCINOMA                24                 36
  RECTAL ADENOCARCINOMA                       135                 11
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   333   4  32  16
  20Q GAIN WILD-TYPE 109   1   5  13
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              333                109
  R1                4                  1
  R2               32                  5
  RX               16                 13
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     7
  20Q GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          45   227
  20Q GAIN WILD-TYPE                        19    65
D37V13, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                  5
  BLACK OR AFRICAN AMERICAN                      45                 19
  WHITE                                         227                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4 262
  20Q GAIN WILD-TYPE   1  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  262
  20Q GAIN WILD-TYPE    1   86
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              262                 86
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    26   7
  21Q GAIN WILD-TYPE 446 114
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                33                560 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                114 
$`21Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-5662 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
       12.66        23.61        24.00         2.01        50.04        47.01 
TCGA-AY-4071 TCGA-AZ-5407 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CM-5868 TCGA-D5-5539 
        0.95        88.21         1.61         3.06        17.03        19.59 
TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M 
        1.48        11.38         6.12        14.04        35.97        95.18 
TCGA-G4-6297 TCGA-NH-A50V TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AG-3611 
       82.39        19.33        29.46        21.90        30.28        13.94 
TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-3885 TCGA-AG-4021 TCGA-AG-A011 TCGA-AH-6644 
       19.99        32.98        17.95         3.98        37.02         0.72 
TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
        9.37         0.49        13.64 

$`21Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01         0.92        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.26        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        16.80        42.77        32.98         8.42        31.30 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       29.98        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         1.45         0.69        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05        33.17         6.97         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       57.24       129.27        24.13        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             95.18             148.01 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            17.950             20.035 
[1] "0.5 - 95.2 (17.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    23  10
  21Q GAIN WILD-TYPE 423 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     23   10
  21Q GAIN WILD-TYPE  423  152
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON                23                423
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q GAIN MUTATED         8        0        1         6         1         0
  21Q GAIN WILD-TYPE      96        1       35       167         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           2          2          5          2        4
  21Q GAIN WILD-TYPE        24         16         78         52       59
                    vv
clus                 STAGE IVA STAGE IVB
  21Q GAIN MUTATED           2         0
  21Q GAIN WILD-TYPE        24         2
D38V4, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   8                 96
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                 6                167
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                2                 16
  STAGE IIIB                5                 78
  STAGE IIIC                2                 52
  STAGE IV                  4                 59
  STAGE IVA                 2                 24
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     3   7  22   2
  21Q GAIN WILD-TYPE  17  99 395  65
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 17
  T2                7                 99
  T3               22                395
  T4                2                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q GAIN MUTATED    16   9   8
  21Q GAIN WILD-TYPE 329 141 107
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               16                329
  N1                9                141
  N2                8                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21   6
  21Q GAIN WILD-TYPE 429  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21    6
  21Q GAIN WILD-TYPE  429   82
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               21                429
  1                6                 82
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18  16
  21Q GAIN WILD-TYPE 269 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18   16
  21Q GAIN WILD-TYPE  269  309
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               18                269
  MALE                 16                309
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    22   2
  21Q GAIN WILD-TYPE 424  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     22    2
  21Q GAIN WILD-TYPE  424   26
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                22                424
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                     18                             5
  21Q GAIN WILD-TYPE                  364                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                      10                              0
  21Q GAIN WILD-TYPE                   136                             13
D38V10, multiclass
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         18                364
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                        10                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    21   0   1   2
  21Q GAIN WILD-TYPE 421   5  36  27
D38V11, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               21                421
  R1                0                  5
  R2                1                 36
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     1
  21Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           5    18
  21Q GAIN WILD-TYPE                        59   274
D38V13, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       5                 59
  WHITE                                          18                274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  22
  21Q GAIN WILD-TYPE   5 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   22
  21Q GAIN WILD-TYPE    5  326
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               22                326
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    18   5
  22Q GAIN WILD-TYPE 454 116
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                570 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                116 
$`22Q GAIN MUTATED`
TCGA-A6-4107 TCGA-A6-6140 TCGA-AA-3494 TCGA-AA-3553 TCGA-AA-3715 TCGA-AA-A02E 
       32.45        24.13         1.02        24.00        19.04         2.96 
TCGA-AZ-4684 TCGA-CK-4948 TCGA-CM-6163 TCGA-CM-6676 TCGA-CM-6679 TCGA-G4-6314 
       65.00       148.01         2.96        11.08        10.06        35.93 
TCGA-RU-A8FL TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 
       30.28        17.23        36.03        19.99        19.99        35.01 
TCGA-AG-3999 TCGA-AG-A00Y TCGA-AH-6897 TCGA-CI-6623 TCGA-DY-A1DF 
       28.04        23.01        26.43         9.37        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.65        32.94         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        13.94        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       19.99        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       46.03        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            148.01             140.38 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.00              19.99 
[1] "1.0 - 148.0 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 433 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   10
  22Q GAIN WILD-TYPE  433  152
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON                13                433
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q GAIN MUTATED         5        0        1         3         0         0
  22Q GAIN WILD-TYPE      99        1       35       170        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           1          0          4          4        4
  22Q GAIN WILD-TYPE        25         18         79         50       59
                    vv
clus                 STAGE IVA STAGE IVB
  22Q GAIN MUTATED           1         0
  22Q GAIN WILD-TYPE        25         2
D39V4, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   5                 99
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                 3                170
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                0                 18
  STAGE IIIB                4                 79
  STAGE IIIC                4                 50
  STAGE IV                  4                 59
  STAGE IVA                 1                 25
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     2   3  18   0
  22Q GAIN WILD-TYPE  18 103 399  67
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                2                 18
  T2                3                103
  T3               18                399
  T4                0                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  22Q GAIN MUTATED    10   6   7
  22Q GAIN WILD-TYPE 335 144 108
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               10                335
  N1                6                144
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    17   5
  22Q GAIN WILD-TYPE 433  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     17    5
  22Q GAIN WILD-TYPE  433   83
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               17                433
  1                5                 83
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10  13
  22Q GAIN WILD-TYPE 277 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10   13
  22Q GAIN WILD-TYPE  277  312
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               10                277
  MALE                 13                312
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    19   0
  22Q GAIN WILD-TYPE 427  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     19    0
  22Q GAIN WILD-TYPE  427   28
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                19                427
  YES                0                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                     13                             0
  22Q GAIN WILD-TYPE                  369                            60
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                      10                              0
  22Q GAIN WILD-TYPE                   136                             13
D39V10, multiclass
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         13                369
  COLON MUCINOUS ADENOCARCINOMA                 0                 60
  RECTAL ADENOCARCINOMA                        10                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    16   0   3   0
  22Q GAIN WILD-TYPE 426   5  34  29
D39V11, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               16                426
  R1                0                  5
  R2                3                 34
  RX                0                 29
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           1    12
  22Q GAIN WILD-TYPE                        63   280
D39V13, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       1                 63
  WHITE                                          12                280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  13
  22Q GAIN WILD-TYPE   5 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   13
  22Q GAIN WILD-TYPE    5  335
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               13                335
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    77  17
  XP GAIN WILD-TYPE 395 104
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               94               499 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               17               104 
$`XP GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-6142 TCGA-A6-6650 
       12.66        44.91        35.11        45.60        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3558 
       24.69        23.87        36.03        29.00        24.00        20.98 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3812 
       54.02        14.01        47.01         5.98         5.03        35.05 
TCGA-AA-3818 TCGA-AA-3844 TCGA-AA-3852 TCGA-AA-3869 TCGA-AA-3966 TCGA-AA-3994 
        0.99        14.93         0.00        27.02         2.01        27.02 
TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-6888 
       31.00        51.98         2.01         0.92        39.98        15.52 
TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-6598 
       16.44        33.01        17.26        18.84        22.36        49.41 
TCGA-AZ-6608 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5860 TCGA-CM-5862 
        1.61        14.30         9.99         1.91        32.02         5.03 
TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6535 
       15.02        21.99        14.99        19.59        55.92        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A28F 
        4.80        17.13        12.49       119.70         7.50        35.97 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 
       98.24        95.18         8.61        74.56        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 
       63.62        39.42        21.90        13.55        10.39        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 
       20.02        86.63        34.03        19.99        19.99        35.01 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       28.04         1.02        46.03        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 
       31.00        38.04         0.72         9.37        78.12        21.01 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1H8 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
        8.98        15.02        32.61        18.28        17.69        13.64 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6235 
       49.51         0.39         0.76        55.76 

$`XP GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.05         6.97         2.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.05        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 
       85.05        26.99        19.04        19.04        10.06        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
       39.06         2.96        39.98         5.03        22.03        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        12.26        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 
       17.75        18.25         1.32        43.27        17.85        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 
       81.37       119.93        60.79       117.07        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       67.30        65.85        53.62        85.48        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30        30.28        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       17.23        43.04        19.10        34.49        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        10.39        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        13.94        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 
       19.99        36.03        14.04        17.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        12.39         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        8.45         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.69         0.53         1.12        12.46        18.28        47.08 
TCGA-G5-6641 
       26.43 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           119.70            148.01 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           20.795            19.990 
[1] "0.0 - 119.7 (20.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    66  31
  XP GAIN WILD-TYPE 380 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     66   31
  XP GAIN WILD-TYPE  380  131
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON               66               380
  RECTUM              31               131
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP GAIN MUTATED        14        0        8        20         1         0
  XP GAIN WILD-TYPE      90        1       28       153         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           3          5         20          8        9
  XP GAIN WILD-TYPE        23         13         63         46       54
                   vv
clus                STAGE IVA STAGE IVB
  XP GAIN MUTATED           9         0
  XP GAIN WILD-TYPE        17         2
D40V4, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 8                28
  STAGE IIA               20               153
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                3                23
  STAGE IIIA               5                13
  STAGE IIIB              20                63
  STAGE IIIC               8                46
  STAGE IV                 9                54
  STAGE IVA                9                17
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED     2  19  71   6
  XP GAIN WILD-TYPE  18  87 346  61
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               2                18
  T2              19                87
  T3              71               346
  T4               6                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XP GAIN MUTATED    48  32  17
  XP GAIN WILD-TYPE 297 118  98
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              48               297
  N1              32               118
  N2              17                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    67  17
  XP GAIN WILD-TYPE 383  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     67   17
  XP GAIN WILD-TYPE  383   71
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              67               383
  1              17                71
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    53  45
  XP GAIN WILD-TYPE 234 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     53   45
  XP GAIN WILD-TYPE  234  280
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              53               234
  MALE                45               280
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    71   4
  XP GAIN WILD-TYPE 375  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     71    4
  XP GAIN WILD-TYPE  375   24
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               71               375
  YES               4                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                     58                             8
  XP GAIN WILD-TYPE                  324                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                      31                              0
  XP GAIN WILD-TYPE                   115                             13
D40V10, multiclass
                                clus
vv                               XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        58               324
  COLON MUCINOUS ADENOCARCINOMA                8                52
  RECTAL ADENOCARCINOMA                       31               115
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    68   1   8   5
  XP GAIN WILD-TYPE 374   4  29  24
D40V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              68               374
  R1               1                 4
  R2               8                29
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     1
  XP GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          12    49
  XP GAIN WILD-TYPE                        52   243
D40V13, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     12                52
  WHITE                                         49               243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  59
  XP GAIN WILD-TYPE   5 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   59
  XP GAIN WILD-TYPE    5  289
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              59               289
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    79  23
  XQ GAIN WILD-TYPE 393  98
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              102               491 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23                98 
$`XQ GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-6142 TCGA-A6-6650 
       12.66        44.91        45.60        37.02        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3553 
       24.69        23.87        56.25        36.03        29.00        24.00 
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3681 
       20.98        78.08        54.02        14.01        47.01         5.98 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3844 TCGA-AA-3852 
        5.03        10.06        35.05         0.99        14.93         0.00 
TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A029 
       27.02        27.02        13.94        31.00        33.04        51.98 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-6888 TCGA-AD-A5EK TCGA-AY-A54L TCGA-AY-A8YK 
        0.92        39.98        15.52        16.44        17.26        18.84 
TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6719 
        5.65        22.36        49.41       100.01         1.61        14.30 
TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 
        9.99        22.98        32.02         5.03        15.02        21.99 
TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       14.99        13.05        19.59        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28F 
       12.49        12.43       119.70         7.50         6.12        35.97 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6306 
       98.24        95.18         8.61         6.18        74.56        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-NH-A6GB TCGA-QL-A97D TCGA-WS-AB45 
       55.04        63.62        39.42        15.65        21.90        70.03 
TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 
       13.55        10.39        16.83        20.02        86.63        34.03 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 
       19.99        19.99        19.04        35.01        28.04         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A032 TCGA-AH-6644 
       46.03        15.95        36.03         9.07        38.04         0.72 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-EI-6510 
        9.37        78.12        21.01         8.98        15.02        18.28 
TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       17.69        13.64         9.96        49.51         0.39         0.76 

$`XQ GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.97         2.01         0.92        50.04        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
       11.01        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        19.04        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13       106.75        65.00        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       30.08        15.02        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
        2.96        29.03        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.85        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 
       81.37       119.93        60.79       117.07        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      133.18        28.21         8.35        82.39        23.51        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        85.48        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33         9.93        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        30.28 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       11.90        24.13        39.48        17.23        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        14.50        15.39        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        13.94        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        36.03        14.04        17.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        3.98        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       37.02         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.56         1.45         0.69        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05        33.17         6.97         4.73        12.39 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.17        11.01        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       11.51        10.78        17.46        11.97         8.45        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           119.70            148.01 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.99             19.99 
[1] "0.0 - 119.7 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76  30
  XQ GAIN WILD-TYPE 370 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76   30
  XQ GAIN WILD-TYPE  370  132
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON               76               370
  RECTUM              30               132
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ GAIN MUTATED        15        0        9        24         1         0
  XQ GAIN WILD-TYPE      89        1       27       149         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           6          4         20         10        7
  XQ GAIN WILD-TYPE        20         14         63         44       56
                   vv
clus                STAGE IVA STAGE IVB
  XQ GAIN MUTATED           9         1
  XQ GAIN WILD-TYPE        17         1
D41V4, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 15                89
  STAGE IA                 0                 1
  STAGE II                 9                27
  STAGE IIA               24               149
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               4                14
  STAGE IIIB              20                63
  STAGE IIIC              10                44
  STAGE IV                 7                56
  STAGE IVA                9                17
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     2  18  79   8
  XQ GAIN WILD-TYPE  18  88 338  59
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                18
  T2              18                88
  T3              79               338
  T4               8                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
  XQ GAIN MUTATED    53  31  22
  XQ GAIN WILD-TYPE 292 119  93
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              53               292
  N1              31               119
  N2              22                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76  16
  XQ GAIN WILD-TYPE 374  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76   16
  XQ GAIN WILD-TYPE  374   72
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              76               374
  1              16                72
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    57  50
  XQ GAIN WILD-TYPE 230 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     57   50
  XQ GAIN WILD-TYPE  230  275
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              57               230
  MALE                50               275
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    81   4
  XQ GAIN WILD-TYPE 365  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     81    4
  XQ GAIN WILD-TYPE  365   24
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               81               365
  YES               4                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                     68                             8
  XQ GAIN WILD-TYPE                  314                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                      29                              0
  XQ GAIN WILD-TYPE                   117                             13
D41V10, multiclass
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        68               314
  COLON MUCINOUS ADENOCARCINOMA                8                52
  RECTAL ADENOCARCINOMA                       29               117
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    79   0   6   5
  XQ GAIN WILD-TYPE 363   5  31  24
D41V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              79               363
  R1               0                 5
  R2               6                31
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          14    53
  XQ GAIN WILD-TYPE                        50   239
D41V13, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     14                50
  WHITE                                         53               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"
D41V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  65
  XQ GAIN WILD-TYPE   5 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   65
  XQ GAIN WILD-TYPE    5  283
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              65               283
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   100  32
  1P LOSS WILD-TYPE 372  89
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              132               461 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32                89 
$`1P LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-3810 TCGA-A6-4105 
        4.80         1.61        43.76        35.11        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3488 
       32.45        29.19        23.61        22.52        21.76         5.03 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 
       38.99         9.07        37.05        19.99        50.04        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3860 
       10.06        38.99        37.02        10.06        33.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       17.03        24.03        12.99         2.01        21.99         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       34.03        42.02        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       26.01         2.01        41.00         0.79         5.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 
        0.20        16.44        14.50        16.31         5.65         5.13 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         3.19        12.69         2.14 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 TCGA-CM-6169 
        1.91         8.02        13.02        22.03        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 
       15.02        11.08        10.06        56.09        17.75         1.32 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-DM-A28A 
        4.80        11.38        92.75        49.91         6.12        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       31.96         1.55        47.41         8.35        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       65.85        35.93        61.91        36.00        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
       10.98         9.93        16.80        11.90        24.13        17.23 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 
       15.39        65.98        11.84        36.03        24.00        34.03 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 
       29.98        37.02        19.04        19.99         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y 
       48.03        19.99        28.04        36.03        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       12.00        70.03        38.96        38.04        38.56         0.69 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       10.19         9.37         4.73        11.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 
       27.95        19.99       126.44       129.27         0.49        20.55 
TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       15.85        11.97        28.57        32.19         0.69        47.08 

$`1P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       15.62        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 
       43.43        42.90        24.33        42.28        44.91        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       13.02         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        36.95        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       15.52        56.55         0.72        27.42        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        28.21        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       44.68        55.04        85.48        63.62        39.42        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       79.69        18.18        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       21.90        30.28        70.03        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        10.39        86.63        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        8.02         7.07        20.05         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3887 
        0.99        32.98         0.99         0.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 
       17.03        13.02        35.01        14.01        32.02        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        41.00         1.45         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       21.01        15.02         8.98        15.02        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       49.51        31.30         0.39         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        26.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.2               0.0 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27            148.01 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            20.27             19.99 
[1] "0.2 - 129.3 (20.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    92  45
  1P LOSS WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     92   45
  1P LOSS WILD-TYPE  354  117
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON               92               354
  RECTUM              45               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P LOSS MUTATED        16        0        5        35         1         0
  1P LOSS WILD-TYPE      88        1       31       138         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           6          4         19         17       24
  1P LOSS WILD-TYPE        20         14         64         37       39
                   vv
clus                STAGE IVA STAGE IVB
  1P LOSS MUTATED           4         0
  1P LOSS WILD-TYPE        22         2
D42V4, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               35               138
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               4                14
  STAGE IIIB              19                64
  STAGE IIIC              17                37
  STAGE IV                24                39
  STAGE IVA                4                22
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED     3  21  96  16
  1P LOSS WILD-TYPE  17  85 321  51
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               3                17
  T2              21                85
  T3              96               321
  T4              16                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1P LOSS MUTATED    62  38  36
  1P LOSS WILD-TYPE 283 112  79
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              62               283
  N1              38               112
  N2              36                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    92  29
  1P LOSS WILD-TYPE 358  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     92   29
  1P LOSS WILD-TYPE  358   59
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              92               358
  1              29                59
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    59  78
  1P LOSS WILD-TYPE 228 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     59   78
  1P LOSS WILD-TYPE  228  247
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              59               228
  MALE                78               247
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    97   8
  1P LOSS WILD-TYPE 349  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     97    8
  1P LOSS WILD-TYPE  349   20
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               97               349
  YES               8                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                     83                             9
  1P LOSS WILD-TYPE                  299                            51
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                      44                              0
  1P LOSS WILD-TYPE                   102                             13
D42V10, multiclass
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        83               299
  COLON MUCINOUS ADENOCARCINOMA                9                51
  RECTAL ADENOCARCINOMA                       44               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    91   1  10   5
  1P LOSS WILD-TYPE 351   4  27  24
D42V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              91               351
  R1               1                 4
  R2              10                27
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  1     2
  1P LOSS WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          18    66
  1P LOSS WILD-TYPE                        46   226
D42V13, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     18                46
  WHITE                                         66               226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  77
  1P LOSS WILD-TYPE   3 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   77
  1P LOSS WILD-TYPE    3  271
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              77               271
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    58  17
  1Q LOSS WILD-TYPE 414 104
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               75               518 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               104 
$`1Q LOSS MUTATED`
TCGA-5M-AAT4 TCGA-A6-5660 TCGA-A6-6138 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
        1.61        29.19        22.52        38.99         9.07        37.05 
TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3851 
       19.99        50.04        10.06        38.99        37.02        33.07 
TCGA-AA-3867 TCGA-AA-3966 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A02W 
       24.03         2.01         7.96        15.02        33.04        41.00 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4614 
        0.79        22.42         0.20        16.44        16.31         5.65 
TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CK-6748 
        5.13        29.56         5.23         3.19         2.14         1.91 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        8.02        13.02        22.03        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A285 
       11.08        10.06        17.75         4.80        11.38         6.12 
TCGA-DM-A28A TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       26.47         1.55         8.35        61.91        36.00        91.79 
TCGA-NH-A50U TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-A56L TCGA-AF-A56N 
       10.98        16.80        11.90        24.13        65.98        11.84 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 
       36.03        24.00        37.02        19.99         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       48.03        19.99        36.03        25.97        23.01        12.00 
TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6511 
       10.19         4.73         5.03        27.95         0.49        15.85 
TCGA-EI-7002 TCGA-F5-6702 TCGA-G5-6572 
       11.97        28.57        47.08 

$`1Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       63.98         6.97         1.02        13.02         1.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        36.95        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        5.79        27.42        10.88         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       25.02        26.04        27.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       12.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       47.41        35.31       133.18        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       85.48        63.62        39.42        35.93        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       79.69        18.18        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        30.28        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99         0.99        19.04        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 
       17.03        13.02        35.01        14.01        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.05        33.17         6.97         9.37        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.17        21.01        11.01        15.02         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              0.2               0.0 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.79            148.01 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           16.310            20.235 
[1] "0.2 - 91.8 (16.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    53  25
  1Q LOSS WILD-TYPE 393 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     53   25
  1Q LOSS WILD-TYPE  393  137
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON               53               393
  RECTUM              25               137
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q LOSS MUTATED        11        0        2        19         1         0
  1Q LOSS WILD-TYPE      93        1       34       154         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           4          3          7          8       15
  1Q LOSS WILD-TYPE        22         15         76         46       48
                   vv
clus                STAGE IVA STAGE IVB
  1Q LOSS MUTATED           3         0
  1Q LOSS WILD-TYPE        23         2
D43V4, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 0                 1
  STAGE II                 2                34
  STAGE IIA               19               154
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                4                22
  STAGE IIIA               3                15
  STAGE IIIB               7                76
  STAGE IIIC               8                46
  STAGE IV                15                48
  STAGE IVA                3                23
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     2  14  54   7
  1Q LOSS WILD-TYPE  18  92 363  60
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               2                18
  T2              14                92
  T3              54               363
  T4               7                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q LOSS MUTATED    37  21  19
  1Q LOSS WILD-TYPE 308 129  96
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              37               308
  N1              21               129
  N2              19                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    49  18
  1Q LOSS WILD-TYPE 401  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     49   18
  1Q LOSS WILD-TYPE  401   70
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              49               401
  1              18                70
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    29  49
  1Q LOSS WILD-TYPE 258 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     29   49
  1Q LOSS WILD-TYPE  258  276
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              29               258
  MALE                49               276
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    56   5
  1Q LOSS WILD-TYPE 390  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     56    5
  1Q LOSS WILD-TYPE  390   23
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               56               390
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                     47                             6
  1Q LOSS WILD-TYPE                  335                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                      25                              0
  1Q LOSS WILD-TYPE                   121                             13
D43V10, multiclass
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        47               335
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       25               121
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    52   1   6   3
  1Q LOSS WILD-TYPE 390   4  31  26
D43V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              52               390
  R1               1                 4
  R2               6                31
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  1     1
  1Q LOSS WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                          13    35
  1Q LOSS WILD-TYPE                        51   257
D43V13, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     13                51
  WHITE                                         35               257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  43
  1Q LOSS WILD-TYPE   3 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   43
  1Q LOSS WILD-TYPE    3  305
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              43               305
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    15   2
  2P LOSS WILD-TYPE 457 119
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               576 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               119 
$`2P LOSS MUTATED`
TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3842 TCGA-AA-3939 TCGA-CA-5797 
        6.97        19.99         2.01        37.02        12.99         3.29 
TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3999 
       15.39        32.02        36.03        13.94        19.04        28.04 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A02X TCGA-EF-5831 TCGA-F5-6571 
       36.03        25.97        41.00         2.40        31.30 

$`2P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         2.14         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       32.02        19.99        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.01              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            41.00            148.01 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            19.99             19.99 
[1] "2.0 - 41.0 (20.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6  11
  2P LOSS WILD-TYPE 440 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6   11
  2P LOSS WILD-TYPE  440  151
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON                6               440
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P LOSS MUTATED         1        0        1         9         0         0
  2P LOSS WILD-TYPE     103        1       35       164        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1          1          1          2        1
  2P LOSS WILD-TYPE        25         17         82         52       62
                   vv
clus                STAGE IVA STAGE IVB
  2P LOSS MUTATED           0         0
  2P LOSS WILD-TYPE        26         2
D44V4, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA                9               164
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               1                17
  STAGE IIIB               1                82
  STAGE IIIC               2                52
  STAGE IV                 1                62
  STAGE IVA                0                26
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     0   2  14   1
  2P LOSS WILD-TYPE  20 104 403  66
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                20
  T2               2               104
  T3              14               403
  T4               1                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2P LOSS MUTATED    11   4   2
  2P LOSS WILD-TYPE 334 146 113
D44V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              11               334
  N1               4               146
  N2               2               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15   1
  2P LOSS WILD-TYPE 435  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15    1
  2P LOSS WILD-TYPE  435   87
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              15               435
  1               1                87
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  10
  2P LOSS WILD-TYPE 280 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   10
  2P LOSS WILD-TYPE  280  315
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               280
  MALE                10               315
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    12   2
  2P LOSS WILD-TYPE 434  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12    2
  2P LOSS WILD-TYPE  434   26
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               12               434
  YES               2                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                      6                             0
  2P LOSS WILD-TYPE                  376                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                       9                              1
  2P LOSS WILD-TYPE                   137                             12
D44V10, multiclass
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         6               376
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    14   0   1   0
  2P LOSS WILD-TYPE 428   5  36  29
D44V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              14               428
  R1               0                 5
  R2               1                36
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     3
  2P LOSS WILD-TYPE                        64   289
D44V13, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                      0                64
  WHITE                                          3               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"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   4
  2P LOSS WILD-TYPE   5 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    4
  2P LOSS WILD-TYPE    5  344
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4               344
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    13   1
  2Q LOSS WILD-TYPE 459 120
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               579 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               120 
$`2Q LOSS MUTATED`
TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3842 TCGA-AA-3939 
        6.97        37.05        19.99         2.01        37.02        12.99 
TCGA-CA-5797 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H 
        3.29        13.94        19.04        28.04        36.03        25.97 
TCGA-AG-A02X TCGA-F5-6571 
       41.00        31.30 

$`2Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        30.28        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       19.99        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
        1.02        48.03        32.02        19.99        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.01              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            41.00            148.01 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            22.98             19.99 
[1] "2.0 - 41.0 (23.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   7
  2Q LOSS WILD-TYPE 439 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    7
  2Q LOSS WILD-TYPE  439  155
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON                7               439
  RECTUM               7               155
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q LOSS MUTATED         1        0        1         8         0         0
  2Q LOSS WILD-TYPE     103        1       35       165        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1          1          0          2        0
  2Q LOSS WILD-TYPE        25         17         83         52       63
                   vv
clus                STAGE IVA STAGE IVB
  2Q LOSS MUTATED           0         0
  2Q LOSS WILD-TYPE        26         2
D45V4, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA                8               165
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               1                17
  STAGE IIIB               0                83
  STAGE IIIC               2                52
  STAGE IV                 0                63
  STAGE IVA                0                26
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     0   2  11   1
  2Q LOSS WILD-TYPE  20 104 406  66
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                20
  T2               2               104
  T3              11               406
  T4               1                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2Q LOSS MUTATED    10   2   2
  2Q LOSS WILD-TYPE 335 148 113
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               335
  N1               2               148
  N2               2               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14   0
  2Q LOSS WILD-TYPE 436  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14    0
  2Q LOSS WILD-TYPE  436   88
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              14               436
  1               0                88
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   9
  2Q LOSS WILD-TYPE 282 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    9
  2Q LOSS WILD-TYPE  282  316
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5               282
  MALE                 9               316
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11   1
  2Q LOSS WILD-TYPE 435  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    1
  2Q LOSS WILD-TYPE  435   27
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               11               435
  YES               1                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                      7                             0
  2Q LOSS WILD-TYPE                  375                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                       6                              0
  2Q LOSS WILD-TYPE                   140                             13
D45V10, multiclass
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         7               375
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        6               140
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   0
  2Q LOSS WILD-TYPE 429   5  37  29
D45V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               429
  R1               0                 5
  R2               0                37
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     1
  2Q LOSS WILD-TYPE                        64   291
D45V13, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               367 
       TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H        TCGA-5M-AAT4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5M-AAT6        TCGA-5M-AATE        TCGA-A6-2671        TCGA-A6-2672 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676        TCGA-A6-2677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2682        TCGA-A6-2683        TCGA-A6-2684        TCGA-A6-2685 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2686        TCGA-A6-3807        TCGA-A6-3810        TCGA-A6-4105 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-4107        TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565        TCGA-A6-A566 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU        TCGA-AD-5900 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6895        TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6964        TCGA-AD-6965        TCGA-AD-A5EJ        TCGA-AD-A5EK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779        TCGA-AU-6004 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L        TCGA-AY-A69D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-A71X        TCGA-AY-A8YK        TCGA-AZ-4308        TCGA-AZ-4313 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4616        TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-6715 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6294        TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6320        TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6627        TCGA-G4-6628        TCGA-NH-A50T        TCGA-NH-A50U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A50V        TCGA-NH-A5IV        TCGA-NH-A6GA        TCGA-NH-A6GB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A6GC        TCGA-NH-A8F7        TCGA-NH-A8F8        TCGA-QG-A5YV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5YW        TCGA-QG-A5YX        TCGA-QG-A5Z1        TCGA-QG-A5Z2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QL-A97D        TCGA-RU-A8FL        TCGA-T9-A92H        TCGA-WS-AB45 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AF-A56K        TCGA-AF-A56L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-A56N        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6702        TCGA-F5-6810 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   2
  2Q LOSS WILD-TYPE   5 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    2
  2Q LOSS WILD-TYPE    5  346
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               346
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    51  16
  3P LOSS WILD-TYPE 421 105
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               526 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               105 
$`3P LOSS MUTATED`
TCGA-5M-AAT4 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-6142 
        1.61        34.65        36.53        14.53        32.45        25.08 
TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3662 
       21.76         9.63         5.03        38.99         9.07         6.05 
TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 
       11.01        85.05        10.06        32.05        31.07        17.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3989 
       29.98        12.99         2.01        21.99        24.00         7.96 
TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K TCGA-AD-A5EK TCGA-AU-3779 TCGA-AZ-4614 
       13.94        32.02        31.00        16.44        14.50         5.65 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 
       12.10         3.29        12.20         1.91         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
        2.96        11.08        11.01        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 
       43.27        17.85         4.80        11.38         7.50        31.96 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-3400 TCGA-AF-4110 
        9.93        42.77        30.28        11.90        34.49        14.50 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-4021 
       20.05        24.00        37.02        19.04        17.95         3.98 
TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6810 
       38.56        10.19         6.05         4.01         5.29         0.39 
TCGA-G5-6233 
       18.28 

$`3P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.25        37.02        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       63.98         6.97         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       34.06        26.01        25.02        27.02        19.07        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        10.88         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.14         3.25         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       79.69        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        37.74        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
        1.45         0.69         0.72        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        27.95        10.98        19.99         5.95         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        55.76        47.08        26.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.39              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            85.05            148.01 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           14.500            20.945 
[1] "0.4 - 85.0 (14.5)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.9"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    54  14
  3P LOSS WILD-TYPE 392 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     54   14
  3P LOSS WILD-TYPE  392  148
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON               54               392
  RECTUM              14               148
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P LOSS MUTATED         5        0        1        21         0         1
  3P LOSS WILD-TYPE      99        1       35       152        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           4          1         10          6       14
  3P LOSS WILD-TYPE        22         17         73         48       49
                   vv
clus                STAGE IVA STAGE IVB
  3P LOSS MUTATED           5         0
  3P LOSS WILD-TYPE        21         2
D46V4, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  5                99
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA               21               152
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                4                22
  STAGE IIIA               1                17
  STAGE IIIB              10                73
  STAGE IIIC               6                48
  STAGE IV                14                49
  STAGE IVA                5                21
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED     2   4  54   9
  3P LOSS WILD-TYPE  18 102 363  58
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                18
  T2               4               102
  T3              54               363
  T4               9                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3P LOSS MUTATED    30  21  18
  3P LOSS WILD-TYPE 315 129  97
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              30               315
  N1              21               129
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    42  19
  3P LOSS WILD-TYPE 408  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     42   19
  3P LOSS WILD-TYPE  408   69
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              42               408
  1              19                69
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    28  41
  3P LOSS WILD-TYPE 259 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     28   41
  3P LOSS WILD-TYPE  259  284
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              28               259
  MALE                41               284
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    54   3
  3P LOSS WILD-TYPE 392  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     54    3
  3P LOSS WILD-TYPE  392   25
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               54               392
  YES               3                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                     50                             4
  3P LOSS WILD-TYPE                  332                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                      10                              3
  3P LOSS WILD-TYPE                   136                             10
D46V10, multiclass
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        50               332
  COLON MUCINOUS ADENOCARCINOMA                4                56
  RECTAL ADENOCARCINOMA                       10               136
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    48   0   8   4
  3P LOSS WILD-TYPE 394   5  29  25
D46V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              48               394
  R1               0                 5
  R2               8                29
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     3
  3P LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           8    32
  3P LOSS WILD-TYPE                        56   260
D46V13, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 9
  BLACK OR AFRICAN AMERICAN                      8                56
  WHITE                                         32               260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  41
  3P LOSS WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   41
  3P LOSS WILD-TYPE    4  307
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              41               307
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    33  10
  3Q LOSS WILD-TYPE 439 111
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               550 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               111 
$`3Q LOSS MUTATED`
TCGA-A6-4105 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3811 
       14.53        32.45        38.99         6.05        85.05        10.06 
TCGA-AA-3855 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       32.05        29.98        12.99         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A01F TCGA-AD-A5EK TCGA-AZ-6600 TCGA-CA-6716 TCGA-CM-4752 
       13.94        32.02        16.44        12.10        12.20        13.02 
TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
        5.03        11.08        11.01        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 
       43.27        17.85         4.80        11.38         7.50        31.96 
TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 
       42.77        30.28        11.90        34.49        14.50        32.02 
TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-4021 TCGA-BM-6198 TCGA-CI-6619 TCGA-DT-5265 
       20.05        37.02         3.98        10.19         6.05         5.29 
TCGA-G5-6233 
       18.28 

$`3Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.61        12.69         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 
       37.02        25.02        26.04         8.02        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        17.85        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        21.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       29.98        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        55.76        47.08        26.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.32              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            85.05            148.01 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            14.50             20.35 
[1] "1.3 - 85.0 (14.5)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    34   9
  3Q LOSS WILD-TYPE 412 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     34    9
  3Q LOSS WILD-TYPE  412  153
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON               34               412
  RECTUM               9               153
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q LOSS MUTATED         3        0        1        16         0         1
  3Q LOSS WILD-TYPE     101        1       35       157        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           2          0          6          3        9
  3Q LOSS WILD-TYPE        24         18         77         51       54
                   vv
clus                STAGE IVA STAGE IVB
  3Q LOSS MUTATED           3         0
  3Q LOSS WILD-TYPE        23         2
D47V4, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  3               101
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA               16               157
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               0                18
  STAGE IIIB               6                77
  STAGE IIIC               3                51
  STAGE IV                 9                54
  STAGE IVA                3                23
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   3  35   6
  3Q LOSS WILD-TYPE  20 103 382  61
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                20
  T2               3               103
  T3              35               382
  T4               6                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3Q LOSS MUTATED    22  11  11
  3Q LOSS WILD-TYPE 323 139 104
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              22               323
  N1              11               139
  N2              11               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    27  11
  3Q LOSS WILD-TYPE 423  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     27   11
  3Q LOSS WILD-TYPE  423   77
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              27               423
  1              11                77
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    16  28
  3Q LOSS WILD-TYPE 271 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16   28
  3Q LOSS WILD-TYPE  271  297
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              16               271
  MALE                28               297
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    34   2
  3Q LOSS WILD-TYPE 412  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     34    2
  3Q LOSS WILD-TYPE  412   26
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               34               412
  YES               2                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                     31                             3
  3Q LOSS WILD-TYPE                  351                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                       5                              4
  3Q LOSS WILD-TYPE                   141                              9
D47V10, multiclass
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        31               351
  COLON MUCINOUS ADENOCARCINOMA                3                57
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    32   0   5   2
  3Q LOSS WILD-TYPE 410   5  32  27
D47V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              32               410
  R1               0                 5
  R2               5                32
  RX               2                27
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     2
  3Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           6    20
  3Q LOSS WILD-TYPE                        58   272
D47V13, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      6                58
  WHITE                                         20               272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  28
  3Q LOSS WILD-TYPE   5 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   28
  3Q LOSS WILD-TYPE    5  320
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              28               320
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   149  39
  4P LOSS WILD-TYPE 323  82
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              188               405 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39                82 
$`4P LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4107 
       35.11        13.94        16.57        37.05        37.02        32.45 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       30.44        29.19        29.16        25.18        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 
       20.28        61.84         9.63         5.03         7.04        38.99 
TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3549 TCGA-AA-3552 
       37.05        34.03        29.00        26.01        21.01        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 
       19.99         6.05         2.01        50.04        15.02        37.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05        10.06        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03        10.06        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3955 
       17.03        24.03        29.98         2.01        12.99        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q 
        2.01        21.99        50.99        26.01        34.03        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        32.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       39.98         2.01        41.00         5.79        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
       14.50         0.95        33.01        17.85         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 
       65.00        12.10        29.56         3.19         2.14         3.29 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5864 TCGA-CM-5868 
       49.08         8.02        29.06        22.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 
        2.96        29.03        13.02        15.02        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.01        10.06        45.40        56.09        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 
        1.32        14.30         9.04         4.80        11.38        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      140.38         7.50        44.32         6.12        14.04        26.47 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 
       16.24        33.67        47.41         8.35        23.51        63.62 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 
       61.91        91.79        46.75        18.18        10.98        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
       42.77        29.46        21.90        11.90        24.13        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       43.04        34.49        37.74        14.50        15.39        65.98 
TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 
       36.03        34.03        34.03        34.03         6.05        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
       19.99        20.98        29.98        37.02        32.98        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
        1.02        17.95        35.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        36.03        14.04        13.94        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       12.00        70.03        41.00         0.69        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       33.17         4.73         5.03        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       19.99       126.44       129.27        32.61         2.40        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.34        16.41        11.97        31.30        28.57         0.39 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

$`4P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       24.33        42.28        45.60        37.25        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       14.53        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3494 
       19.66        16.24        24.92        56.25         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 
        8.05        19.07         0.00        19.07        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       15.95        14.93         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       32.05        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00         2.01        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
       35.01        37.02        39.06        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
       16.44         0.46         0.92        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41        32.94       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        13.02        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02         5.03        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       11.08        12.03        12.26        19.59        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.43         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       13.32       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        34.42        41.42        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        12.79        17.85        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       31.30        30.28        70.03        39.48        13.55        19.10 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       10.39        16.83        20.02        10.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 
        0.99        19.99        36.95        17.03        13.02        14.01 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       32.02         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        38.04        38.56         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
       26.43         1.81         6.97         9.37        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.17        21.01        11.01        15.02         8.98        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       17.00        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19         0.66         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              0.2               0.0 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           140.38            148.01 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           21.385            19.330 
[1] "0.2 - 140.4 (21.4)" "0.0 - 148.0 (19.3)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   135  58
  4P LOSS WILD-TYPE 311 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    135   58
  4P LOSS WILD-TYPE  311  104
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON              135               311
  RECTUM              58               104
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P LOSS MUTATED        26        0        6        51         2         0
  4P LOSS WILD-TYPE      78        1       30       122         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           7          8         26         22       31
  4P LOSS WILD-TYPE        19         10         57         32       32
                   vv
clus                STAGE IVA STAGE IVB
  4P LOSS MUTATED          11         1
  4P LOSS WILD-TYPE        15         1
D48V4, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 26                78
  STAGE IA                 0                 1
  STAGE II                 6                30
  STAGE IIA               51               122
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                7                19
  STAGE IIIA               8                10
  STAGE IIIB              26                57
  STAGE IIIC              22                32
  STAGE IV                31                32
  STAGE IVA               11                15
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED     6  30 135  24
  4P LOSS WILD-TYPE  14  76 282  43
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               6                14
  T2              30                76
  T3             135               282
  T4              24                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P LOSS MUTATED    91  56  48
  4P LOSS WILD-TYPE 254  94  67
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              91               254
  N1              56                94
  N2              48                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   128  42
  4P LOSS WILD-TYPE 322  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    128   42
  4P LOSS WILD-TYPE  322   46
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             128               322
  1              42                46
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    88 107
  4P LOSS WILD-TYPE 199 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     88  107
  4P LOSS WILD-TYPE  199  218
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              88               199
  MALE               107               218
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   138  15
  4P LOSS WILD-TYPE 308  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    138   15
  4P LOSS WILD-TYPE  308   13
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              138               308
  YES              15                13
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                    125                            10
  4P LOSS WILD-TYPE                  257                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                      54                              3
  4P LOSS WILD-TYPE                    92                             10
D48V10, multiclass
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       125               257
  COLON MUCINOUS ADENOCARCINOMA               10                50
  RECTAL ADENOCARCINOMA                       54                92
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   141   0  15   6
  4P LOSS WILD-TYPE 301   5  22  23
D48V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             141               301
  R1               0                 5
  R2              15                22
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          23    90
  4P LOSS WILD-TYPE                        41   202
D48V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     23                41
  WHITE                                         90               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     3 104
  4P LOSS WILD-TYPE   2 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3  104
  4P LOSS WILD-TYPE    2  244
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             104               244
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   144  37
  4Q LOSS WILD-TYPE 328  84
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              181               412 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37                84 
$`4Q LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 
        4.80         1.61        39.45        43.76        43.43        35.11 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 
       13.94        16.57        37.05        32.45        29.19        29.16 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       21.76        23.87        20.28        61.84         9.63         5.03 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3548 
       38.99        37.05        34.03        29.00        26.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 
       21.01        13.02        19.99         6.05         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 
       37.05        36.00        85.05        10.06        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 
       37.02        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       17.03         2.01        20.98         2.01        21.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F 
       26.01        24.00        34.03        42.02        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 
       33.04        26.01         2.96        39.98        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D 
       22.42         0.20        14.50        16.31         0.95        17.85 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 
        5.65         5.13        65.00        12.10        29.56         2.14 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       14.30        49.08         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
        5.03        15.02        17.03         2.96        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6926 TCGA-D5-6929 
       20.19        17.75         1.32        43.27         9.04         4.80 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      140.38         7.50        44.32         6.12        14.04        26.47 
TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 
       31.96        16.24        47.41         8.35        23.51        63.62 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       61.91        91.79        46.75        18.18        10.98         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 
       16.80        42.77        29.46        21.90        11.90        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 
       14.50        15.39        65.98        36.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 
        6.05        13.94        19.99        20.98        29.98        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       19.04         1.02        17.95         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        36.03        14.04        13.94        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
       12.00        70.03        64.01        41.00        38.56         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
       10.19         6.05        33.17         4.73        11.01         5.03 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        27.95        10.98        19.99       126.44       129.27 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
        2.40        17.00        15.85        16.34        16.41        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

$`4Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 
       24.33        42.28        44.91        45.60        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       20.61        24.69        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92        56.25         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07         0.00        19.07        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       14.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       14.93         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       12.26        19.59        55.92        20.42        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       12.59       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.79        17.85        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       30.28        70.03        39.48        10.39        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       32.02         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        38.04         1.45         0.72        26.43         1.81 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        12.39        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02         8.98        13.97         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        0.49        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        8.45         9.96        49.51         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       12.46        18.28        55.76        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              0.2               0.0 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.38            148.01 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           20.280            19.975 
[1] "0.2 - 140.4 (20.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   122  62
  4Q LOSS WILD-TYPE 324 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    122   62
  4Q LOSS WILD-TYPE  324  100
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON              122               324
  RECTUM              62               100
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q LOSS MUTATED        25        0        6        51         1         0
  4Q LOSS WILD-TYPE      79        1       30       122         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           7          7         28         25       24
  4Q LOSS WILD-TYPE        19         11         55         29       39
                   vv
clus                STAGE IVA STAGE IVB
  4Q LOSS MUTATED          10         0
  4Q LOSS WILD-TYPE        16         2
D49V4, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 25                79
  STAGE IA                 0                 1
  STAGE II                 6                30
  STAGE IIA               51               122
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                7                19
  STAGE IIIA               7                11
  STAGE IIIB              28                55
  STAGE IIIC              25                29
  STAGE IV                24                39
  STAGE IVA               10                16
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED     5  29 130  24
  4Q LOSS WILD-TYPE  15  77 287  43
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                15
  T2              29                77
  T3             130               287
  T4              24                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4Q LOSS MUTATED    88  56  44
  4Q LOSS WILD-TYPE 257  94  71
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              88               257
  N1              56                94
  N2              44                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   128  34
  4Q LOSS WILD-TYPE 322  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    128   34
  4Q LOSS WILD-TYPE  322   54
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             128               322
  1              34                54
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    85 103
  4Q LOSS WILD-TYPE 202 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     85  103
  4Q LOSS WILD-TYPE  202  222
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              85               202
  MALE               103               222
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   134  14
  4Q LOSS WILD-TYPE 312  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    134   14
  4Q LOSS WILD-TYPE  312   14
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              134               312
  YES              14                14
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                    111                            11
  4Q LOSS WILD-TYPE                  271                            49
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                      58                              3
  4Q LOSS WILD-TYPE                    88                             10
D49V10, multiclass
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       111               271
  COLON MUCINOUS ADENOCARCINOMA               11                49
  RECTAL ADENOCARCINOMA                       58                88
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   136   1  11   7
  4Q LOSS WILD-TYPE 306   4  26  22
D49V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             136               306
  R1               1                 4
  R2              11                26
  RX               7                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          24    91
  4Q LOSS WILD-TYPE                        40   201
D49V13, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     24                40
  WHITE                                         91               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"
D49V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 105
  4Q LOSS WILD-TYPE   2 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  105
  4Q LOSS WILD-TYPE    2  243
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             105               243
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    63  20
  5P LOSS WILD-TYPE 409 101
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               83               510 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               20               101 
$`5P LOSS MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2682 
        1.61        39.45        43.76        43.76        42.28        13.94 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 
       36.53        14.53        29.19        32.71        27.09        25.18 
TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3673 
       24.16        23.87         9.63         5.03        26.01        50.04 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3941 
       10.06        36.95        10.06        33.07        36.03        24.00 
TCGA-AA-3966 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
        2.01        34.03        27.02        42.02        10.98        33.04 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-A54L TCGA-AZ-4614 
       41.00        22.42         0.20        16.31        17.26         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 
       65.00        62.79         5.23        49.08         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6172 
       22.03         5.03        15.02         2.96        29.03        11.01 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-G4-6295 TCGA-G4-6317 
       17.85         4.41        12.43         9.04         8.35        36.00 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2691 
       18.18        10.98        42.77        21.90        24.13        43.04 
TCGA-AF-6136 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3882 
       15.39         6.05        13.94        20.98        37.02        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A01W 
        1.02        48.03        28.04         3.98        23.01        70.03 
TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD 
       33.17        13.97        27.95        10.98       126.44        57.24 
TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7004 TCGA-G5-6233 
       20.55        16.41        13.64         8.45        18.28 

$`5P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       42.90        24.33        44.91        35.11        45.60        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       29.16        22.52        24.13         8.38        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        56.25         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
        0.00        17.03         0.00         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41        32.94         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         1.48         3.68        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      133.18        28.21        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        61.91        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       79.69        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        16.80        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       30.28        11.90        70.03        39.48        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        8.98        15.02        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46        11.97         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.2               0.0 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            148.01 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.03             19.99 
[1] "0.2 - 126.4 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    59  27
  5P LOSS WILD-TYPE 387 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     59   27
  5P LOSS WILD-TYPE  387  135
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON               59               387
  RECTUM              27               135
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P LOSS MUTATED        15        0        4        15         0         2
  5P LOSS WILD-TYPE      89        1       32       158        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           4          5         12         11        8
  5P LOSS WILD-TYPE        22         13         71         43       55
                   vv
clus                STAGE IVA STAGE IVB
  5P LOSS MUTATED           8         0
  5P LOSS WILD-TYPE        18         2
D50V4, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 15                89
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               15               158
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                4                22
  STAGE IIIA               5                13
  STAGE IIIB              12                71
  STAGE IIIC              11                43
  STAGE IV                 8                55
  STAGE IVA                8                18
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     3  15  57  11
  5P LOSS WILD-TYPE  17  91 360  56
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               3                17
  T2              15                91
  T3              57               360
  T4              11                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
  5P LOSS MUTATED    39  27  20
  5P LOSS WILD-TYPE 306 123  95
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              39               306
  N1              27               123
  N2              20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    60  15
  5P LOSS WILD-TYPE 390  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     60   15
  5P LOSS WILD-TYPE  390   73
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              60               390
  1              15                73
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    43  43
  5P LOSS WILD-TYPE 244 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     43   43
  5P LOSS WILD-TYPE  244  282
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              43               244
  MALE                43               282
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    70   4
  5P LOSS WILD-TYPE 376  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     70    4
  5P LOSS WILD-TYPE  376   24
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               70               376
  YES               4                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                     54                             5
  5P LOSS WILD-TYPE                  328                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                      26                              1
  5P LOSS WILD-TYPE                   120                             12
D50V10, multiclass
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        54               328
  COLON MUCINOUS ADENOCARCINOMA                5                55
  RECTAL ADENOCARCINOMA                       26               120
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    59   1   3   3
  5P LOSS WILD-TYPE 383   4  34  26
D50V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              59               383
  R1               1                 4
  R2               3                34
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          11    47
  5P LOSS WILD-TYPE                        53   245
D50V13, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                     11                53
  WHITE                                         47               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"
D50V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  51
  5P LOSS WILD-TYPE   2 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   51
  5P LOSS WILD-TYPE    2  297
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              51               297
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    86  31
  5Q LOSS WILD-TYPE 386  90
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              117               476 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31                90 
$`5Q LOSS MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2686 
        1.61        39.45        43.76        43.76        13.94        37.02 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6648 
       36.53        14.53        30.44        29.19        27.09        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 
       24.16        21.76        23.87         9.63         5.03        26.01 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3697 TCGA-AA-3811 
       12.99        13.02        19.99        50.04        85.05        10.06 
TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3941 
       36.95        10.06        33.07        31.07        24.03        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D 
        2.01        21.99        34.03        27.02        42.02        10.98 
TCGA-AA-A01T TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       33.04         2.01        41.00        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 
       16.31        17.26         5.65        65.00        62.79         5.23 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5344 
        1.61         3.29        14.30        49.08         8.02        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6536 
        5.03        15.02         2.96        29.03        13.02        17.85 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1DB TCGA-DM-A285 
        4.41        12.43         9.04         4.80        44.32         6.12 
TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-G4-6625 
        8.61         1.55         8.35        82.39        36.00        91.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       18.18        10.98        42.77        21.90        30.28        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AG-3578 
       17.23        43.04        37.74        15.39        86.63        32.02 
TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
       13.94        20.98        29.98        37.02        32.98        19.04 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 
       19.99         1.02        48.03        28.04        36.03        17.03 
TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
        3.98        23.01        70.03        64.01         1.94        38.96 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       10.19        33.17         5.03        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 
       10.98         4.01       126.44        57.24        51.48        20.55 
TCGA-EI-6881 TCGA-F5-6702 TCGA-G5-6233 
       16.41        28.57        18.28 

$`5Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 
       16.57        37.05        37.25        34.65        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       29.16        22.52        24.13         8.38        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       14.93         0.00        17.03         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
       15.52        56.55         0.79         0.72         5.79        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        75.95        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
      100.01        29.56        11.74         3.19        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       17.75        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       47.41        35.31       133.18        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       63.62        39.42        35.93        61.91        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       79.69        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        16.80        29.46        32.98         8.42        31.30 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       11.90        70.03        39.48        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       10.39        14.50        16.83        20.02        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       35.01        14.01        32.02        19.99        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       46.03        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
        7.17        21.01        11.01        15.02         8.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
        5.95         5.03         5.29        41.36       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        12.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.2               0.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            148.01 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            21.99             19.81 
[1] "0.2 - 126.4 (22.0)" "0.0 - 148.0 (19.8)"
[1] "hr=" "1.4"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    80  41
  5Q LOSS WILD-TYPE 366 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     80   41
  5Q LOSS WILD-TYPE  366  121
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON               80               366
  RECTUM              41               121
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q LOSS MUTATED        18        0        6        27         0         1
  5Q LOSS WILD-TYPE      86        1       30       146        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           4          5         16         17       14
  5Q LOSS WILD-TYPE        22         13         67         37       49
                   vv
clus                STAGE IVA STAGE IVB
  5Q LOSS MUTATED          10         0
  5Q LOSS WILD-TYPE        16         2
D51V4, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 18                86
  STAGE IA                 0                 1
  STAGE II                 6                30
  STAGE IIA               27               146
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                4                22
  STAGE IIIA               5                13
  STAGE IIIB              16                67
  STAGE IIIC              17                37
  STAGE IV                14                49
  STAGE IVA               10                16
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     3  19  87  12
  5Q LOSS WILD-TYPE  17  87 330  55
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               3                17
  T2              19                87
  T3              87               330
  T4              12                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5Q LOSS MUTATED    57  31  33
  5Q LOSS WILD-TYPE 288 119  82
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              57               288
  N1              31               119
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    80  24
  5Q LOSS WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     80   24
  5Q LOSS WILD-TYPE  370   64
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              80               370
  1              24                64
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    54  67
  5Q LOSS WILD-TYPE 233 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     54   67
  5Q LOSS WILD-TYPE  233  258
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              54               233
  MALE                67               258
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    93   5
  5Q LOSS WILD-TYPE 353  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     93    5
  5Q LOSS WILD-TYPE  353   23
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               93               353
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                     73                             7
  5Q LOSS WILD-TYPE                  309                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                      39                              1
  5Q LOSS WILD-TYPE                   107                             12
D51V10, multiclass
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        73               309
  COLON MUCINOUS ADENOCARCINOMA                7                53
  RECTAL ADENOCARCINOMA                       39               107
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    82   2   7   4
  5Q LOSS WILD-TYPE 360   3  30  25
D51V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              82               360
  R1               2                 3
  R2               7                30
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     2
  5Q LOSS WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          15    59
  5Q LOSS WILD-TYPE                        49   233
D51V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     15                49
  WHITE                                         59               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"
D51V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  69
  5Q LOSS WILD-TYPE   2 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   69
  5Q LOSS WILD-TYPE    2  279
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              69               279
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    32  12
  6P LOSS WILD-TYPE 440 109
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               44               549 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               109 
$`6P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3561 
       43.76        42.28        37.02        24.16        20.28        13.94 
TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3875 
        2.01        36.00        19.04        38.99        36.95        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A01X TCGA-AD-6899 
       12.99        24.00         2.01        18.05        26.01         5.79 
TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       16.44         5.65         3.19        12.69         3.06         2.14 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6898 
       11.08        11.01        45.40        20.19        17.75         1.48 
TCGA-DM-A1D7 TCGA-F4-6808 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3591 
       13.32        33.67        17.23        13.55        34.49        34.03 
TCGA-AG-3593 TCGA-AG-3611 TCGA-AG-A008 TCGA-AG-A011 TCGA-DC-6682 TCGA-DT-5265 
       34.03        13.94        13.94        37.02         4.01         5.29 
TCGA-DY-A1DF TCGA-EI-6883 
       24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        24.33        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       11.74         1.61         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        30.28        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       19.99        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       27.95        10.98        19.99         5.95         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.48              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            45.40            148.01 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            17.49             20.05 
[1] "1.5 - 45.4 (17.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    33  11
  6P LOSS WILD-TYPE 413 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33   11
  6P LOSS WILD-TYPE  413  151
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON               33               413
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P LOSS MUTATED         7        0        2        20         1         1
  6P LOSS WILD-TYPE      97        1       34       153         9         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           2          0          3          3        3
  6P LOSS WILD-TYPE        24         18         80         51       60
                   vv
clus                STAGE IVA STAGE IVB
  6P LOSS MUTATED           3         0
  6P LOSS WILD-TYPE        23         2
D52V4, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  7                97
  STAGE IA                 0                 1
  STAGE II                 2                34
  STAGE IIA               20               153
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               0                18
  STAGE IIIB               3                80
  STAGE IIIC               3                51
  STAGE IV                 3                60
  STAGE IVA                3                23
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED     2   6  30   7
  6P LOSS WILD-TYPE  18 100 387  60
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                18
  T2               6               100
  T3              30               387
  T4               7                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6P LOSS MUTATED    30   8   7
  6P LOSS WILD-TYPE 315 142 108
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              30               315
  N1               8               142
  N2               7               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    34   6
  6P LOSS WILD-TYPE 416  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     34    6
  6P LOSS WILD-TYPE  416   82
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              34               416
  1               6                82
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    19  26
  6P LOSS WILD-TYPE 268 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     19   26
  6P LOSS WILD-TYPE  268  299
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              19               268
  MALE                26               299
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    33   5
  6P LOSS WILD-TYPE 413  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33    5
  6P LOSS WILD-TYPE  413   23
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               33               413
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                     27                             5
  6P LOSS WILD-TYPE                  355                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                       8                              3
  6P LOSS WILD-TYPE                   138                             10
D52V10, multiclass
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        27               355
  COLON MUCINOUS ADENOCARCINOMA                5                55
  RECTAL ADENOCARCINOMA                        8               138
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    31   0   1   6
  6P LOSS WILD-TYPE 411   5  36  23
D52V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              31               411
  R1               0                 5
  R2               1                36
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     4
  6P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    23
  6P LOSS WILD-TYPE                        63   269
D52V13, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 8
  BLACK OR AFRICAN AMERICAN                      1                63
  WHITE                                         23               269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  26
  6P LOSS WILD-TYPE   5 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   26
  6P LOSS WILD-TYPE    5  322
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              26               322
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    50  16
  6Q LOSS WILD-TYPE 422 105
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               66               527 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               105 
$`6Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3552 
       43.76        42.28        32.45        24.16        20.28        13.02 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 
       13.94        61.02         2.01        36.00        19.04        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        31.07        29.98        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02H 
        2.01         2.01        18.05        10.98        26.01         2.01 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        5.79        16.44         0.46         3.19        12.69         3.06 
TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
        2.14        11.01        13.05        11.08        11.01        45.40 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6704 
       20.19        17.75        15.12         1.48        13.32         1.55 
TCGA-F4-6808 TCGA-NH-A6GA TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       33.67         9.93        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       34.49        12.00        32.02        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A011 
       34.03         6.05        13.94        14.04        13.94        37.02 
TCGA-AH-6544 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6883 TCGA-G5-6233 TCGA-G5-6641 
       38.56         4.01         5.29        11.51        18.28        26.43 

$`6Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        24.33        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        24.03        27.02        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        0.72        22.42        27.42        10.88         0.20         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.61         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       14.04        12.95        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        30.28        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       39.48        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 
        8.02         7.07        36.03        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02        17.03         3.98        46.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.95         5.03       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        55.76        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            61.02            148.01 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           16.835            20.550 
[1] "0.5 - 61.0 (16.8)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.7"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    45  21
  6Q LOSS WILD-TYPE 401 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     45   21
  6Q LOSS WILD-TYPE  401  141
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON               45               401
  RECTUM              21               141
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q LOSS MUTATED        10        0        4        20         1         2
  6Q LOSS WILD-TYPE      94        1       32       153         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           2          1          7          9        7
  6Q LOSS WILD-TYPE        24         17         76         45       56
                   vv
clus                STAGE IVA STAGE IVB
  6Q LOSS MUTATED           3         1
  6Q LOSS WILD-TYPE        23         1
D53V4, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 10                94
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               20               153
  STAGE IIB                1                 9
  STAGE IIC                2                 1
  STAGE III                2                24
  STAGE IIIA               1                17
  STAGE IIIB               7                76
  STAGE IIIC               9                45
  STAGE IV                 7                56
  STAGE IVA                3                23
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED     4   8  48   8
  6Q LOSS WILD-TYPE  16  98 369  59
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               4                16
  T2               8                98
  T3              48               369
  T4               8                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
  6Q LOSS MUTATED    35  13  20
  6Q LOSS WILD-TYPE 310 137  95
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              35               310
  N1              13               137
  N2              20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    46  12
  6Q LOSS WILD-TYPE 404  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     46   12
  6Q LOSS WILD-TYPE  404   76
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              46               404
  1              12                76
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    27  41
  6Q LOSS WILD-TYPE 260 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27   41
  6Q LOSS WILD-TYPE  260  284
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              27               260
  MALE                41               284
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    49   7
  6Q LOSS WILD-TYPE 397  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     49    7
  6Q LOSS WILD-TYPE  397   21
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               49               397
  YES               7                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                     37                             7
  6Q LOSS WILD-TYPE                  345                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                      16                              5
  6Q LOSS WILD-TYPE                   130                              8
D53V10, multiclass
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        37               345
  COLON MUCINOUS ADENOCARCINOMA                7                53
  RECTAL ADENOCARCINOMA                       16               130
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    50   0   3   7
  6Q LOSS WILD-TYPE 392   5  34  22
D53V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              50               392
  R1               0                 5
  R2               3                34
  RX               7                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     4
  6Q LOSS WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    29
  6Q LOSS WILD-TYPE                        61   263
D53V13, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 8
  BLACK OR AFRICAN AMERICAN                      3                61
  WHITE                                         29               263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  34
  6Q LOSS WILD-TYPE   5 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   34
  6Q LOSS WILD-TYPE    5  314
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              34               314
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 469 121
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               590 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0               121 
$`7P LOSS MUTATED`
TCGA-5M-AATE TCGA-D5-6932 TCGA-AG-A008 
       39.45        11.38        13.94 

$`7P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       15.62         4.80        12.66         1.61         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        5.79        22.42        27.42        10.88         0.20        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        30.28        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            11.38              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            39.45            148.01 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.94             19.99 
[1] "11.4 - 39.5 (13.9)" "0.0 - 148.0 (20.0)"
[1] "hr="     "3300000"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 444 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  444  161
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  COLON                2               444
  RECTUM               1               161
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7P LOSS MUTATED         1        0        0         2         0         0
  7P LOSS WILD-TYPE     103        1       36       171        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           0          0          0          0        0
  7P LOSS WILD-TYPE        26         18         83         54       63
                   vv
clus                STAGE IVA STAGE IVB
  7P LOSS MUTATED           0         0
  7P LOSS WILD-TYPE        26         2
D54V4, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 0                36
  STAGE IIA                2               171
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                0                26
  STAGE IIIA               0                18
  STAGE IIIB               0                83
  STAGE IIIC               0                54
  STAGE IV                 0                63
  STAGE IVA                0                26
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     0   1   2   0
  7P LOSS WILD-TYPE  20 105 415  67
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                20
  T2               1               105
  T3               2               415
  T4               0                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7P LOSS MUTATED     3   0   0
  7P LOSS WILD-TYPE 342 150 115
D54V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               3               342
  N1               0               150
  N2               0               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 447  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  447   88
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3               447
  1               0                88
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   2
  7P LOSS WILD-TYPE 286 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE  286  323
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               1               286
  MALE                 2               323
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 443  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  443   28
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                3               443
  YES               0                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P LOSS MUTATED                      2                             0
  7P LOSS WILD-TYPE                  380                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7P LOSS MUTATED                       0                              1
  7P LOSS WILD-TYPE                   146                             12
D54V10, multiclass
                                clus
vv                               7P LOSS MUTATED 7P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         2               380
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        0               146
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED     3   0   0   0
  7P LOSS WILD-TYPE 439   5  37  29
D54V11, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               3               439
  R1               0                 5
  R2               0                37
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1     1
  7P LOSS WILD-TYPE                        63   291
D54V13, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               367 
       TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H        TCGA-5M-AAT4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-5M-AAT6        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-2675        TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-2683        TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-2686 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-3807        TCGA-A6-3810        TCGA-A6-4105        TCGA-A6-4107 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137        TCGA-A6-6138 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142        TCGA-A6-6648 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651        TCGA-A6-6652 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-6782        TCGA-A6-A565        TCGA-A6-A566        TCGA-A6-A567 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-A6-A56B        TCGA-A6-A5ZU        TCGA-AD-5900        TCGA-AD-6548 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AD-6965        TCGA-AD-A5EJ        TCGA-AD-A5EK        TCGA-AM-5820 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AM-5821        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AY-6386        TCGA-AY-A54L        TCGA-AY-A69D        TCGA-AY-A71X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AY-A8YK        TCGA-AZ-4308        TCGA-AZ-4313        TCGA-AZ-4315 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280        TCGA-DM-A282 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6294 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298        TCGA-G4-6299 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6311 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6586 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6627 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G4-6628        TCGA-NH-A50T        TCGA-NH-A50U        TCGA-NH-A50V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-NH-A5IV        TCGA-NH-A6GA        TCGA-NH-A6GB        TCGA-NH-A6GC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-NH-A8F7        TCGA-NH-A8F8        TCGA-QG-A5YV        TCGA-QG-A5YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QG-A5YX        TCGA-QG-A5Z1        TCGA-QG-A5Z2        TCGA-QL-A97D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-RU-A8FL        TCGA-T9-A92H        TCGA-WS-AB45        TCGA-AF-2687 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691        TCGA-AF-2692 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911        TCGA-AF-3913 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AF-6672        TCGA-AF-A56K        TCGA-AF-A56L        TCGA-AF-A56N 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6623 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6464 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D54V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   1
  7P LOSS WILD-TYPE   4 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    1
  7P LOSS WILD-TYPE    4  347
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               1               347
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5   0
  7Q LOSS WILD-TYPE 467 121
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               588 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0               121 
$`7Q LOSS MUTATED`
TCGA-5M-AATE TCGA-CM-5341 TCGA-D5-6932 TCGA-AG-3591 TCGA-AG-A008 
       39.45        29.06        11.38        34.03        13.94 

$`7Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       15.62         4.80        12.66         1.61         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        5.79        22.42        27.42        10.88         0.20        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        30.28        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02        17.03         3.98        46.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            11.38              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            39.45            148.01 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            29.06             19.99 
[1] "11.4 - 39.5 (29.1)" "0.0 - 148.0 (20.0)"
[1] "hr="     "3300000"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   2
  7Q LOSS WILD-TYPE 443 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    2
  7Q LOSS WILD-TYPE  443  160
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON                3               443
  RECTUM               2               160
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q LOSS MUTATED         1        0        0         3         0         0
  7Q LOSS WILD-TYPE     103        1       36       170        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          1          0          0        0
  7Q LOSS WILD-TYPE        26         17         83         54       63
                   vv
clus                STAGE IVA STAGE IVB
  7Q LOSS MUTATED           0         0
  7Q LOSS WILD-TYPE        26         2
D55V4, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 0                36
  STAGE IIA                3               170
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                0                26
  STAGE IIIA               1                17
  STAGE IIIB               0                83
  STAGE IIIC               0                54
  STAGE IV                 0                63
  STAGE IVA                0                26
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     0   2   3   0
  7Q LOSS WILD-TYPE  20 104 414  67
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                20
  T2               2               104
  T3               3               414
  T4               0                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7Q LOSS MUTATED     4   1   0
  7Q LOSS WILD-TYPE 341 149 115
D55V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               4               341
  N1               1               149
  N2               0               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     5   0
  7Q LOSS WILD-TYPE 445  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    0
  7Q LOSS WILD-TYPE  445   88
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               5               445
  1               0                88
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   2
  7Q LOSS WILD-TYPE 284 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    2
  7Q LOSS WILD-TYPE  284  323
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3               284
  MALE                 2               323
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4   1
  7Q LOSS WILD-TYPE 442  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    1
  7Q LOSS WILD-TYPE  442   27
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                4               442
  YES               1                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                      3                             0
  7Q LOSS WILD-TYPE                  379                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                       1                              1
  7Q LOSS WILD-TYPE                   145                             12
D55V10, multiclass
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         3               379
  COLON MUCINOUS ADENOCARCINOMA                0                60
  RECTAL ADENOCARCINOMA                        1               145
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     5   0   0   0
  7Q LOSS WILD-TYPE 437   5  37  29
D55V11, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               5               437
  R1               0                 5
  R2               0                37
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                1    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           1     2
  7Q LOSS WILD-TYPE                        63   290
D55V13, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      1                63
  WHITE                                          2               290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE   4 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE    4  346
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2               346
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   166  46
  8P LOSS WILD-TYPE 306  75
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              212               381 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               46                75 
$`8P LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        4.80         9.53        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       44.91        35.11        45.60        16.57        34.65        36.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       32.91        30.44        23.61        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 
       56.25         5.03        37.05         1.02        38.99        24.03 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
        0.00        34.03        26.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3666 
       24.00        23.01        19.99        19.99        78.08         2.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3860 TCGA-AA-3866 
       36.00        85.05        37.02        33.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3971 
       24.03        27.02         2.01        24.00        34.03        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       34.06        26.01        24.00        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       34.03         1.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 
       37.02        41.00        22.42         0.20        16.31        33.01 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6600 
       17.85       109.28         5.65       106.75        62.79        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4952 
       29.56        11.74         1.61         3.29        14.30        15.62 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
        2.96        21.99        13.02        15.02        13.05        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       10.06        12.26        56.09        43.27        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
       15.58         4.41         9.04         4.80        11.38       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       49.91        13.32       140.38       131.51         6.12        26.47 
TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 
       60.79        31.96        35.74         1.55        34.42         0.53 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       23.51        74.56        35.93        61.91        36.00        26.43 
TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QL-A97D 
       91.79        10.98        19.33         9.93        16.80        21.90 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       30.28        39.48        17.23        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       10.39        15.39        10.39        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 
       46.03        34.03        34.03        34.03         2.01         6.05 
TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
        0.99        13.94         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3909 TCGA-AG-3999 
        0.99         1.02        17.03        35.01        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       36.03        14.04        17.03        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       15.95         1.02        12.00        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 
       38.96        41.00         1.45         0.72        10.19         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       12.39        78.12        21.01        11.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       27.95        10.98         5.03         5.29       126.44       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 
       51.48         2.40        15.85        16.34        10.78        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
        8.45         9.96        31.30        28.57         0.69        12.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`8P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         1.61        39.45        46.65        42.90 
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       24.33        13.94        37.05        37.25        37.02        14.53 
TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.45        31.63        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       32.71        29.16        22.52         8.38        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       24.39        20.12        19.66        16.24        24.92         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        7.04         3.02         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 
        6.97         1.02        13.02         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       12.99         0.99        14.01        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        0.92        50.04        47.05         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 
        2.01        21.99        50.99        13.05        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09         0.95        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84        75.95        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        88.21        49.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23         3.19        12.69         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5861 
       25.02        26.04         8.02        27.02        29.06        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.01        12.03        45.40        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       20.19        20.42        17.75        18.25         1.32        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.80        17.13        16.14         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
      119.70        24.43        38.20        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 
       11.11        35.74         6.18        47.87        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 
       55.04        85.48        63.62        39.42        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
       18.18        19.33        15.65        12.79        17.85        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 
       29.46        32.98         8.42        31.30        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       24.13        43.04        34.49        14.50        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
        8.02         7.07        20.05        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3881 
       19.99        19.99        20.98        37.02         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
       19.99        17.95        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
       13.94         6.02        36.03         9.07        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       64.01        49.97        61.97        38.04        38.56         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81         6.05        33.17         6.97         9.37 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
        7.17        15.02         8.98        15.02        19.99         5.95 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        4.01        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        13.64        17.46 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       49.51         0.39        32.19         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           140.38            148.01 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           21.945            19.590 
[1] "0.0 - 140.4 (21.9)" "0.0 - 148.0 (19.6)"
[1] "hr=" "1.2"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   141  73
  8P LOSS WILD-TYPE 305  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    141   73
  8P LOSS WILD-TYPE  305   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON              141               305
  RECTUM              73                89
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P LOSS MUTATED        29        0        9        51         2         1
  8P LOSS WILD-TYPE      75        1       27       122         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED          11          9         30         24       32
  8P LOSS WILD-TYPE        15          9         53         30       31
                   vv
clus                STAGE IVA STAGE IVB
  8P LOSS MUTATED          12         1
  8P LOSS WILD-TYPE        14         1
D56V4, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 29                75
  STAGE IA                 0                 1
  STAGE II                 9                27
  STAGE IIA               51               122
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III               11                15
  STAGE IIIA               9                 9
  STAGE IIIB              30                53
  STAGE IIIC              24                30
  STAGE IV                32                31
  STAGE IVA               12                14
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED     3  34 154  25
  8P LOSS WILD-TYPE  17  72 263  42
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                17
  T2              34                72
  T3             154               263
  T4              25                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8P LOSS MUTATED    99  61  55
  8P LOSS WILD-TYPE 246  89  60
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              99               246
  N1              61                89
  N2              55                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   148  43
  8P LOSS WILD-TYPE 302  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    148   43
  8P LOSS WILD-TYPE  302   45
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             148               302
  1              43                45
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    92 124
  8P LOSS WILD-TYPE 195 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     92  124
  8P LOSS WILD-TYPE  195  201
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              92               195
  MALE               124               201
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   157  13
  8P LOSS WILD-TYPE 289  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    157   13
  8P LOSS WILD-TYPE  289   15
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              157               289
  YES              13                15
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                    127                            12
  8P LOSS WILD-TYPE                  255                            48
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                      67                              5
  8P LOSS WILD-TYPE                    79                              8
D56V10, multiclass
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       127               255
  COLON MUCINOUS ADENOCARCINOMA               12                48
  RECTAL ADENOCARCINOMA                       67                79
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   153   2  17   5
  8P LOSS WILD-TYPE 289   3  20  24
D56V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             153               289
  R1               2                 3
  R2              17                20
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     3
  8P LOSS WILD-TYPE                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          24   100
  8P LOSS WILD-TYPE                        40   192
D56V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 9
  BLACK OR AFRICAN AMERICAN                     24                40
  WHITE                                        100               192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3 120
  8P LOSS WILD-TYPE   2 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3  120
  8P LOSS WILD-TYPE    2  228
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             120               228
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27   8
  8Q LOSS WILD-TYPE 445 113
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               558 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8               113 
$`8Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-6782 
       43.76        43.76        44.91        16.57        34.65        20.28 
TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3851 TCGA-AA-3941 TCGA-AA-3989 TCGA-AD-6901 
       38.99        34.03        33.07        24.00         7.96        22.42 
TCGA-AD-6965 TCGA-AY-A69D TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6679 TCGA-D5-5538 
        0.20        17.85        62.79        32.02        10.06        12.26 
TCGA-D5-6539 TCGA-DM-A1D6 TCGA-F4-6704 TCGA-G4-6625 TCGA-QL-A97D TCGA-AG-3611 
       12.49        49.91         1.55        91.79        21.90        13.94 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6644 
        1.02        17.03        23.01        12.00        41.00         0.72 
TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 TCGA-G5-6233 
       27.95        51.48        15.85         0.69        18.28 

$`8Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       45.60        13.94        37.05        37.25        37.02        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
        0.79         0.72         5.79        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        65.00        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        19.99        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         1.45         0.69        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98        13.97        15.02        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       31.30        28.57         0.39        32.19         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.2               0.0 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.79            148.01 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            21.90             19.99 
[1] "0.2 - 91.8 (21.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    24  12
  8Q LOSS WILD-TYPE 422 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     24   12
  8Q LOSS WILD-TYPE  422  150
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON               24               422
  RECTUM              12               150
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q LOSS MUTATED         5        0        1        10         2         1
  8Q LOSS WILD-TYPE      99        1       35       163         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          1          3          4        4
  8Q LOSS WILD-TYPE        26         17         80         50       59
                   vv
clus                STAGE IVA STAGE IVB
  8Q LOSS MUTATED           2         0
  8Q LOSS WILD-TYPE        24         2
D57V4, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  5                99
  STAGE IA                 0                 1
  STAGE II                 1                35
  STAGE IIA               10               163
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III                0                26
  STAGE IIIA               1                17
  STAGE IIIB               3                80
  STAGE IIIC               4                50
  STAGE IV                 4                59
  STAGE IVA                2                24
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     0   5  26   5
  8Q LOSS WILD-TYPE  20 101 391  62
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                20
  T2               5               101
  T3              26               391
  T4               5                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
  8Q LOSS MUTATED    21   5   9
  8Q LOSS WILD-TYPE 324 145 106
D57V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              21               324
  N1               5               145
  N2               9               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   6
  8Q LOSS WILD-TYPE 429  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    6
  8Q LOSS WILD-TYPE  429   82
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              21               429
  1               6                82
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  26
  8Q LOSS WILD-TYPE 277 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   26
  8Q LOSS WILD-TYPE  277  299
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               277
  MALE                26               299
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    24   1
  8Q LOSS WILD-TYPE 422  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     24    1
  8Q LOSS WILD-TYPE  422   27
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               24               422
  YES               1                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                     20                             4
  8Q LOSS WILD-TYPE                  362                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                      12                              0
  8Q LOSS WILD-TYPE                   134                             13
D57V10, multiclass
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        20               362
  COLON MUCINOUS ADENOCARCINOMA                4                56
  RECTAL ADENOCARCINOMA                       12               134
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    27   0   1   0
  8Q LOSS WILD-TYPE 415   5  36  29
D57V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              27               415
  R1               0                 5
  R2               1                36
  RX               0                29
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     0
  8Q LOSS WILD-TYPE                                0    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           3    21
  8Q LOSS WILD-TYPE                        61   271
D57V13, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      3                61
  WHITE                                         21               271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  21
  8Q LOSS WILD-TYPE   5 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   21
  8Q LOSS WILD-TYPE    5  327
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              21               327
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    56  17
  9P LOSS WILD-TYPE 416 104
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               73               520 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17               104 
$`9P LOSS MUTATED`
TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 
       39.45        43.43        36.53        14.53        29.16        24.16 
TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3553 TCGA-AA-3562 
       21.76        61.84         6.97        38.99        24.00        19.99 
TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       37.05        85.05        24.03        12.99        24.00        20.98 
TCGA-AA-3972 TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A03J TCGA-AD-6888 
       50.99        13.94        32.02        31.00        40.96        15.52 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-6605 TCGA-AZ-6607 
        0.20        14.50        16.31         5.65         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-6169 TCGA-CM-6170 
        1.61         3.29        12.20         8.02        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       11.08        11.01        10.06        20.19         1.32        43.27 
TCGA-D5-6898 TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA 
        1.48        38.20        33.67         8.35        82.39         9.93 
TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 
       16.80        11.90        24.13        13.55        65.98        20.05 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4021 TCGA-AG-A014 
       34.03         6.05        37.02        19.99         3.98        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 
       12.00        31.00         1.94        38.96         6.05         4.73 
TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DG TCGA-EF-5830 
       12.39        11.01        10.98        19.99        51.48         0.49 
TCGA-EI-6514 
       16.31 

$`9P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       15.62         4.80        12.66         1.61         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.02        34.65        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       58.03        63.98         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98         1.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
        0.72         5.79        22.42        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       75.95        58.39         1.41        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10       100.01        29.56        11.74        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.14         3.25         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       12.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        17.85        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        30.28        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       70.03        64.01        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19        33.17         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        27.95         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              0.2               0.0 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            85.05            148.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            16.31             20.35 
[1] "0.2 - 85.0 (16.3)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.4"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    53  22
  9P LOSS WILD-TYPE 393 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     53   22
  9P LOSS WILD-TYPE  393  140
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON               53               393
  RECTUM              22               140
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P LOSS MUTATED        13        0        4        18         1         0
  9P LOSS WILD-TYPE      91        1       32       155         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           2          3          9          8       13
  9P LOSS WILD-TYPE        24         15         74         46       50
                   vv
clus                STAGE IVA STAGE IVB
  9P LOSS MUTATED           4         0
  9P LOSS WILD-TYPE        22         2
D58V4, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               18               155
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                2                24
  STAGE IIIA               3                15
  STAGE IIIB               9                74
  STAGE IIIC               8                46
  STAGE IV                13                50
  STAGE IVA                4                22
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED     2  16  45  13
  9P LOSS WILD-TYPE  18  90 372  54
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                18
  T2              16                90
  T3              45               372
  T4              13                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9P LOSS MUTATED    39  19  18
  9P LOSS WILD-TYPE 306 131  97
D58V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              39               306
  N1              19               131
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    53  17
  9P LOSS WILD-TYPE 397  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     53   17
  9P LOSS WILD-TYPE  397   71
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              53               397
  1              17                71
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  47
  9P LOSS WILD-TYPE 258 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   47
  9P LOSS WILD-TYPE  258  278
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29               258
  MALE                47               278
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    58   3
  9P LOSS WILD-TYPE 388  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     58    3
  9P LOSS WILD-TYPE  388   25
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               58               388
  YES               3                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                     51                             1
  9P LOSS WILD-TYPE                  331                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                      21                              1
  9P LOSS WILD-TYPE                   125                             12
D58V10, multiclass
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        51               331
  COLON MUCINOUS ADENOCARCINOMA                1                59
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    49   2   8   3
  9P LOSS WILD-TYPE 393   3  29  26
D58V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              49               393
  R1               2                 3
  R2               8                29
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           8    37
  9P LOSS WILD-TYPE                        56   255
D58V13, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      8                56
  WHITE                                         37               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"
D58V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  43
  9P LOSS WILD-TYPE   3 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   43
  9P LOSS WILD-TYPE    3  305
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              43               305
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    57  16
  9Q LOSS WILD-TYPE 415 105
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               73               520 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               16               105 
$`9Q LOSS MUTATED`
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6142 
       39.45        43.76        43.43        36.53        29.16        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3553 
       24.16        21.76        61.84         6.97        38.99        24.00 
TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3955 
       19.99        37.05        85.05        24.03        12.99        20.98 
TCGA-AA-3972 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A03J TCGA-AU-3779 TCGA-AY-4070 
       50.99        32.02        31.00        40.96        14.50        16.31 
TCGA-AY-4071 TCGA-AZ-4614 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        0.95         5.65        29.56         5.23         3.19         1.61 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6169 
        3.29        12.20         8.02        13.02        22.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 
       15.02        11.08        11.01        10.06        20.19         1.32 
TCGA-D5-6898 TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
        1.48        38.20        33.67         8.35        82.39        65.85 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L 
        9.93        16.80        11.90        24.13        13.55        65.98 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-A014 
       20.05        34.03        37.02        19.99        36.03        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 
       12.00        31.00         1.94        38.96         6.05         4.73 
TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 TCGA-EI-6514 
       12.39        11.01        10.98        19.99         0.49        16.31 
TCGA-F5-6702 
       28.57 

$`9Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       15.62         4.80        12.66         1.61         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       10.88         0.20        16.44         0.46         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 
       49.41         6.77        12.10       100.01        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.08        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        12.26        19.59        56.09        55.92        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        23.51        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       79.69        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        30.28        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       16.83        15.39        20.02        10.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       70.03        64.01        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19        33.17         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        27.95         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        31.30         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.49              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            85.05            148.01 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           19.990            20.005 
[1] "0.5 - 85.0 (20.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D59V2, continuous
D59V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    53  22
  9Q LOSS WILD-TYPE 393 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     53   22
  9Q LOSS WILD-TYPE  393  140
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON               53               393
  RECTUM              22               140
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q LOSS MUTATED        14        0        4        17         1         0
  9Q LOSS WILD-TYPE      90        1       32       156         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           2          3         10          7       14
  9Q LOSS WILD-TYPE        24         15         73         47       49
                   vv
clus                STAGE IVA STAGE IVB
  9Q LOSS MUTATED           4         0
  9Q LOSS WILD-TYPE        22         2
D59V4, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               17               156
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                2                24
  STAGE IIIA               3                15
  STAGE IIIB              10                73
  STAGE IIIC               7                47
  STAGE IV                14                49
  STAGE IVA                4                22
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED     3  17  45  12
  9Q LOSS WILD-TYPE  17  89 372  55
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               3                17
  T2              17                89
  T3              45               372
  T4              12                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9Q LOSS MUTATED    39  22  16
  9Q LOSS WILD-TYPE 306 128  99
D59V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              39               306
  N1              22               128
  N2              16                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    52  18
  9Q LOSS WILD-TYPE 398  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     52   18
  9Q LOSS WILD-TYPE  398   70
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              52               398
  1              18                70
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    32  45
  9Q LOSS WILD-TYPE 255 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     32   45
  9Q LOSS WILD-TYPE  255  280
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              32               255
  MALE                45               280
[1] 2 2
[1] FALSE
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    61   2
  9Q LOSS WILD-TYPE 385  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     61    2
  9Q LOSS WILD-TYPE  385   26
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               61               385
  YES               2                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                     51                             1
  9Q LOSS WILD-TYPE                  331                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                      21                              1
  9Q LOSS WILD-TYPE                   125                             12
D59V10, multiclass
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        51               331
  COLON MUCINOUS ADENOCARCINOMA                1                59
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    51   2   8   3
  9Q LOSS WILD-TYPE 391   3  29  26
D59V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              51               391
  R1               2                 3
  R2               8                29
  RX               3                26
[1] 4 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, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           9    39
  9Q LOSS WILD-TYPE                        55   253
D59V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      9                55
  WHITE                                         39               253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  46
  9Q LOSS WILD-TYPE   2 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   46
  9Q LOSS WILD-TYPE    2  302
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              46               302
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    84  14
  10P LOSS WILD-TYPE 388 107
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                98                495 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                107 
$`10P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       24.33        35.11        45.60        30.44        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       22.52        25.18        23.87         9.63         1.02         6.97 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       13.02        19.99        50.04        37.05        36.00        85.05 
TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-3989 
       10.06        31.07        17.03        24.03        50.99         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 
       34.03        42.02        10.98        26.01        41.00        22.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 
       16.44        14.50         5.65         5.13        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 
       29.56         3.19         3.29        12.20        14.30         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       29.06        22.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6898 TCGA-D5-6926 
       15.02        11.08        11.08        17.75         1.48         9.04 
TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 
        4.80        82.39        65.85        55.04        61.91        26.04 
TCGA-G4-6626 TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 
       46.75        12.79        17.85        30.28        24.13        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       34.49        10.39        65.98        46.03        34.03        34.03 
TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00H 
       29.98        36.95         1.02        19.99        13.94        25.97 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-CI-6624 TCGA-DC-6155 
       12.00        10.98        41.00        38.56         4.73        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 
       15.02        27.95         4.01         5.03       129.27         0.49 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7004 TCGA-F5-6702 
       17.00        16.34        16.31        16.41         8.45        28.57 
TCGA-F5-6864 TCGA-G5-6641 
       12.46        26.43 

$`10P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        56.25         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       33.04        35.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
      109.28        75.95        58.39         1.41        32.94       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       63.62        39.42        35.93        36.00        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        11.90        70.03        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02        17.03         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        64.01        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.96        61.97        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03         8.98        10.98        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         9.96        49.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.49               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             148.01 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             21.01              19.99 
[1] "0.5 - 129.3 (21.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    66  33
  10P LOSS WILD-TYPE 380 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     66   33
  10P LOSS WILD-TYPE  380  129
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON                66                380
  RECTUM               33                129
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P LOSS MUTATED        16        0        5        20         1         1
  10P LOSS WILD-TYPE      88        1       31       153         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           3          5         16         10       13
  10P LOSS WILD-TYPE        23         13         67         44       50
                    vv
clus                 STAGE IVA STAGE IVB
  10P LOSS MUTATED           6         1
  10P LOSS WILD-TYPE        20         1
D60V4, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  16                 88
  STAGE IA                  0                  1
  STAGE II                  5                 31
  STAGE IIA                20                153
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                5                 13
  STAGE IIIB               16                 67
  STAGE IIIC               10                 44
  STAGE IV                 13                 50
  STAGE IVA                 6                 20
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED     2  20  67  11
  10P LOSS WILD-TYPE  18  86 350  56
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                2                 18
  T2               20                 86
  T3               67                350
  T4               11                 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
  10P LOSS MUTATED    47  30  23
  10P LOSS WILD-TYPE 298 120  92
D60V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               47                298
  N1               30                120
  N2               23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    70  19
  10P LOSS WILD-TYPE 380  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     70   19
  10P LOSS WILD-TYPE  380   69
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               70                380
  1               19                 69
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46  54
  10P LOSS WILD-TYPE 241 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46   54
  10P LOSS WILD-TYPE  241  271
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               46                241
  MALE                 54                271
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    74  11
  10P LOSS WILD-TYPE 372  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     74   11
  10P LOSS WILD-TYPE  372   17
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                74                372
  YES               11                 17
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                     60                             6
  10P LOSS WILD-TYPE                  322                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                      27                              6
  10P LOSS WILD-TYPE                   119                              7
D60V10, multiclass
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         60                322
  COLON MUCINOUS ADENOCARCINOMA                 6                 54
  RECTAL ADENOCARCINOMA                        27                119
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    75   0   6   5
  10P LOSS WILD-TYPE 367   5  31  24
D60V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               75                367
  R1                0                  5
  R2                6                 31
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     3
  10P LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           9    56
  10P LOSS WILD-TYPE                        55   236
D60V13, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                       9                 55
  WHITE                                          56                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  64
  10P LOSS WILD-TYPE   4 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   64
  10P LOSS WILD-TYPE    4  284
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               64                284
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    92  16
  10Q LOSS WILD-TYPE 380 105
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               108                485 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                16                105 
$`10Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 
       43.76        24.33        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3494 
       29.16        22.52        25.18        23.87         9.63         1.02 
TCGA-AA-3511 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3673 
        6.97        33.99        13.02        19.99         6.05        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3858 
       37.05        36.00        85.05        36.95        10.06        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D 
       17.03        24.03        50.99        34.03        42.02        10.98 
TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
       26.01        41.00        22.42        16.44        14.50        16.31 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
        5.65        65.00        62.79        29.56         3.19         3.29 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       12.20        14.30         8.02        29.06        22.03         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6926 
       11.08        10.06        17.75        43.27         1.48         9.04 
TCGA-D5-6929 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 
        4.80        33.67        55.04        61.91        26.04        91.79 
TCGA-G4-6626 TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 
       46.75        12.79        17.85        30.28        24.13        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 
       34.49        10.39        65.98        32.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 
       34.03         6.05        29.98        36.95         1.02        19.99 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
       13.94        25.97        37.02        12.00        10.98        41.00 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
        4.73        13.97        27.95         4.01         5.03       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       24.13         0.49        17.00        16.34        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       11.97        28.57         0.66        12.46        47.08        26.43 

$`10Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       61.84        56.25         5.03         7.04         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        10.88         0.20         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13       106.75        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         2.14         3.25         0.07        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       55.92        20.19        20.42        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       85.48        63.62        39.42        35.93        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        11.90        70.03        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       13.94        19.99        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       17.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 
        3.98        46.03        20.98         6.02        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
       10.19         6.05        33.17         6.97         9.37        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
        8.98        15.02        10.98        19.99         5.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30         0.39        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        18.28        55.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             148.01 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             22.47              19.99 
[1] "0.5 - 129.3 (22.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    72  37
  10Q LOSS WILD-TYPE 374 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     72   37
  10Q LOSS WILD-TYPE  374  125
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON                72                374
  RECTUM               37                125
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q LOSS MUTATED        17        0        5        27         1         1
  10Q LOSS WILD-TYPE      87        1       31       146         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           3          5         16         13       13
  10Q LOSS WILD-TYPE        23         13         67         41       50
                    vv
clus                 STAGE IVA STAGE IVB
  10Q LOSS MUTATED           5         1
  10Q LOSS WILD-TYPE        21         1
D61V4, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  0                  1
  STAGE II                  5                 31
  STAGE IIA                27                146
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                5                 13
  STAGE IIIB               16                 67
  STAGE IIIC               13                 41
  STAGE IV                 13                 50
  STAGE IVA                 5                 21
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED     3  20  75  11
  10Q LOSS WILD-TYPE  17  86 342  56
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                3                 17
  T2               20                 86
  T3               75                342
  T4               11                 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
  10Q LOSS MUTATED    55  29  25
  10Q LOSS WILD-TYPE 290 121  90
D61V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               55                290
  N1               29                121
  N2               25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    81  18
  10Q LOSS WILD-TYPE 369  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     81   18
  10Q LOSS WILD-TYPE  369   70
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               81                369
  1               18                 70
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    50  60
  10Q LOSS WILD-TYPE 237 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     50   60
  10Q LOSS WILD-TYPE  237  265
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               50                237
  MALE                 60                265
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    81  12
  10Q LOSS WILD-TYPE 365  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     81   12
  10Q LOSS WILD-TYPE  365   16
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                81                365
  YES               12                 16
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                     66                             6
  10Q LOSS WILD-TYPE                  316                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                      31                              6
  10Q LOSS WILD-TYPE                   115                              7
D61V10, multiclass
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         66                316
  COLON MUCINOUS ADENOCARCINOMA                 6                 54
  RECTAL ADENOCARCINOMA                        31                115
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    83   1   7   5
  10Q LOSS WILD-TYPE 359   4  30  24
D61V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               83                359
  R1                1                  4
  R2                7                 30
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          10    59
  10Q LOSS WILD-TYPE                        54   233
D61V13, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      10                 54
  WHITE                                          59                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"
D61V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  69
  10Q LOSS WILD-TYPE   4 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   69
  10Q LOSS WILD-TYPE    4  279
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               69                279
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    60  11
  11P LOSS WILD-TYPE 412 110
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                71                522 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                110 
$`11P LOSS MUTATED`
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 
       36.53        32.45        30.44        22.52        24.16        21.76 
TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3855 
        9.07         6.05         2.01        37.05        36.00        32.05 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 
       31.07        12.99        24.00         2.01         2.01        21.99 
TCGA-AA-3972 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E 
       50.99        42.02        32.02        31.00        33.04         2.96 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4323 
       40.96         5.79        16.44        14.50        17.85         1.41 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
        2.14        12.20        49.08         5.03        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6924 
        2.96        11.01        45.40        20.19        43.27        14.30 
TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC TCGA-AF-2691 
        7.50        61.91        36.00        18.18        12.79        43.04 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3600 
       14.50        15.39        10.39        32.02         7.07         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L 
       32.98        19.04        17.95         1.02        13.94        12.00 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 
       10.98        41.00        38.56         0.69        13.97        15.02 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
        5.29        24.13        17.00        16.41         0.69 

$`11P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00         2.01        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98         1.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       32.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        74.79        79.69        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       11.90        70.03        24.13        39.48        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       19.10        34.49        37.74        10.39        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       86.63        65.98        11.84        36.03        12.00         8.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        37.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02        17.03         3.98        46.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        1.94        38.96        61.97        38.04         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02         5.03         8.98        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39        32.19         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.69               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             61.91             148.01 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             16.44              20.20 
[1] "0.7 - 61.9 (16.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  23
  11P LOSS WILD-TYPE 396 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   23
  11P LOSS WILD-TYPE  396  139
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON                50                396
  RECTUM               23                139
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P LOSS MUTATED        15        0        2        14         0         0
  11P LOSS WILD-TYPE      89        1       34       159        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           5          2         10         11        8
  11P LOSS WILD-TYPE        21         16         73         43       55
                    vv
clus                 STAGE IVA STAGE IVB
  11P LOSS MUTATED           5         1
  11P LOSS WILD-TYPE        21         1
D62V4, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  15                 89
  STAGE IA                  0                  1
  STAGE II                  2                 34
  STAGE IIA                14                159
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 5                 21
  STAGE IIIA                2                 16
  STAGE IIIB               10                 73
  STAGE IIIC               11                 43
  STAGE IV                  8                 55
  STAGE IVA                 5                 21
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED     2  14  46  12
  11P LOSS WILD-TYPE  18  92 371  55
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 18
  T2               14                 92
  T3               46                371
  T4               12                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11P LOSS MUTATED    30  24  20
  11P LOSS WILD-TYPE 315 126  95
D62V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               30                315
  N1               24                126
  N2               20                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  13
  11P LOSS WILD-TYPE 400  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   13
  11P LOSS WILD-TYPE  400   75
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               50                400
  1               13                 75
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    34  40
  11P LOSS WILD-TYPE 253 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     34   40
  11P LOSS WILD-TYPE  253  285
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               34                253
  MALE                 40                285
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    54   5
  11P LOSS WILD-TYPE 392  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     54    5
  11P LOSS WILD-TYPE  392   23
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                54                392
  YES                5                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                     43                             7
  11P LOSS WILD-TYPE                  339                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                      18                              4
  11P LOSS WILD-TYPE                   128                              9
D62V10, multiclass
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         43                339
  COLON MUCINOUS ADENOCARCINOMA                 7                 53
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    53   0   5   4
  11P LOSS WILD-TYPE 389   5  32  25
D62V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               53                389
  R1                0                  5
  R2                5                 32
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     3
  11P LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           4    35
  11P LOSS WILD-TYPE                        60   257
D62V13, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                       4                 60
  WHITE                                          35                257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  38
  11P LOSS WILD-TYPE   5 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   38
  11P LOSS WILD-TYPE    5  310
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               38                310
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    72  17
  11Q LOSS WILD-TYPE 400 104
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                89                504 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                104 
$`11Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 
       43.76        16.57        36.53        32.45        30.44        22.52 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3662 
       24.16        21.76        23.87         6.97         9.07         6.05 
TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 
        2.01        36.00        32.05        31.07        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-A00Q TCGA-AA-A01F 
       24.00         2.01        21.99        50.99        42.02        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6899 
       31.00        33.04         2.96        39.98        40.96         5.79 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A69D TCGA-AY-A71X 
       22.42        16.44        14.50         0.95        17.85        19.33 
TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5862 
        1.41         2.14        12.20         1.91        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-5537 
       15.02        15.02         2.96        11.01        11.01        45.40 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1D6 
       20.19        43.27        17.85        14.30       130.65        49.91 
TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC TCGA-AF-2691 
        7.50        61.91        36.00        18.18        12.79        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 
       13.55        19.10        14.50        15.39        10.39        32.02 
TCGA-AG-3581 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3732 
        7.07        34.03         2.01         6.05        13.94        32.98 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 
       19.04        17.95         1.02        13.94        12.00        10.98 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 
       38.56         0.69        10.19        12.39        13.97        10.98 
TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 
       19.99         5.29        24.13        17.00        16.41 

$`11Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       37.02        34.65        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
       63.98         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       36.03         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       24.00        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72        27.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       17.26        18.84       109.28        75.95        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        74.79        79.69        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        17.85        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 
       11.90        70.03        24.13        39.48        17.23        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        12.00         8.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       24.00         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 
       12.03         0.99        15.95        19.99        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.72        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37         4.73        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02         5.03         8.98        15.02        27.95 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.69               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            130.65             148.01 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             17.00              20.76 
[1] "0.7 - 130.7 (17.0)" "0.0 - 148.0 (20.8)"
[1] "hr=" "1.2"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    61  27
  11Q LOSS WILD-TYPE 385 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     61   27
  11Q LOSS WILD-TYPE  385  135
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON                61                385
  RECTUM               27                135
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q LOSS MUTATED        19        0        2        21         0         0
  11Q LOSS WILD-TYPE      85        1       34       152        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           5          3         13         10       12
  11Q LOSS WILD-TYPE        21         15         70         44       51
                    vv
clus                 STAGE IVA STAGE IVB
  11Q LOSS MUTATED           4         1
  11Q LOSS WILD-TYPE        22         1
D63V4, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  19                 85
  STAGE IA                  0                  1
  STAGE II                  2                 34
  STAGE IIA                21                152
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 5                 21
  STAGE IIIA                3                 15
  STAGE IIIB               13                 70
  STAGE IIIC               10                 44
  STAGE IV                 12                 51
  STAGE IVA                 4                 22
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED     4  16  60  12
  11Q LOSS WILD-TYPE  16  90 357  55
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 16
  T2               16                 90
  T3               60                357
  T4               12                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11Q LOSS MUTATED    43  30  19
  11Q LOSS WILD-TYPE 302 120  96
D63V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               43                302
  N1               30                120
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    62  16
  11Q LOSS WILD-TYPE 388  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     62   16
  11Q LOSS WILD-TYPE  388   72
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               62                388
  1               16                 72
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    46  46
  11Q LOSS WILD-TYPE 241 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     46   46
  11Q LOSS WILD-TYPE  241  279
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               46                241
  MALE                 46                279
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    70   7
  11Q LOSS WILD-TYPE 376  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     70    7
  11Q LOSS WILD-TYPE  376   21
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                70                376
  YES                7                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                     53                             8
  11Q LOSS WILD-TYPE                  329                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                      21                              5
  11Q LOSS WILD-TYPE                   125                              8
D63V10, multiclass
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         53                329
  COLON MUCINOUS ADENOCARCINOMA                 8                 52
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    65   0   6   4
  11Q LOSS WILD-TYPE 377   5  31  25
D63V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               65                377
  R1                0                  5
  R2                6                 31
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     3
  11Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    48
  11Q LOSS WILD-TYPE                        59   244
D63V13, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                       5                 59
  WHITE                                          48                244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  51
  11Q LOSS WILD-TYPE   4 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   51
  11Q LOSS WILD-TYPE    4  297
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               51                297
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    49  19
  12P LOSS WILD-TYPE 423 102
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                68                525 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                19                102 
$`12P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-6782 
       43.76        45.60        34.65        36.53        30.44        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3666 
       61.84         9.63        26.01        33.99        13.02         2.01 
TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       50.04        31.07        17.03        24.03         2.01        50.99 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       32.02        33.04         2.96         5.79        22.42        16.44 
TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
       65.00         2.14        49.08         8.02         5.03         2.96 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 
       29.03        15.02        11.01        11.08        10.06         1.32 
TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 
       11.38        12.59         7.50        31.96        16.24        65.85 
TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-3913 
       61.91        36.00        17.85        30.28        43.04        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 
       14.50        15.39        34.03        34.03        29.98        48.03 
TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 
        3.98        23.01        70.03        10.19        13.97        10.98 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
       24.13        51.48        20.91        17.00        16.31        16.41 
TCGA-F5-6702 TCGA-F5-6812 
       28.57         0.66 

$`12P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       37.02        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       20.12        19.66        16.24        24.92        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        14.01        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.65        32.94         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       13.55        19.10        34.49        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       46.03        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72        26.43         1.81         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02         5.03         8.98        15.02        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24       129.27        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        19.96        18.28        15.85        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        31.30         0.39        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.66               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             148.01 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            20.595             19.990 
[1] "0.7 - 70.0 (20.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    46  23
  12P LOSS WILD-TYPE 400 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     46   23
  12P LOSS WILD-TYPE  400  139
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON                46                400
  RECTUM               23                139
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P LOSS MUTATED        10        0        2        15         1         0
  12P LOSS WILD-TYPE      94        1       34       158         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          3         10         11        9
  12P LOSS WILD-TYPE        24         15         73         43       54
                    vv
clus                 STAGE IVA STAGE IVB
  12P LOSS MUTATED           5         0
  12P LOSS WILD-TYPE        21         2
D64V4, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  10                 94
  STAGE IA                  0                  1
  STAGE II                  2                 34
  STAGE IIA                15                158
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                3                 15
  STAGE IIIB               10                 73
  STAGE IIIC               11                 43
  STAGE IV                  9                 54
  STAGE IVA                 5                 21
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     3   9  54   4
  12P LOSS WILD-TYPE  17  97 363  63
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 17
  T2                9                 97
  T3               54                363
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P LOSS MUTATED    30  23  17
  12P LOSS WILD-TYPE 315 127  98
D64V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               30                315
  N1               23                127
  N2               17                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    45  13
  12P LOSS WILD-TYPE 405  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     45   13
  12P LOSS WILD-TYPE  405   75
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               45                405
  1               13                 75
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    34  36
  12P LOSS WILD-TYPE 253 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     34   36
  12P LOSS WILD-TYPE  253  289
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               34                253
  MALE                 36                289
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    53   5
  12P LOSS WILD-TYPE 393  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     53    5
  12P LOSS WILD-TYPE  393   23
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                53                393
  YES                5                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                     45                             1
  12P LOSS WILD-TYPE                  337                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                      23                              0
  12P LOSS WILD-TYPE                   123                             13
D64V10, multiclass
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         45                337
  COLON MUCINOUS ADENOCARCINOMA                 1                 59
  RECTAL ADENOCARCINOMA                        23                123
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    54   0   4   2
  12P LOSS WILD-TYPE 388   5  33  27
D64V11, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               54                388
  R1                0                  5
  R2                4                 33
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           6    41
  12P LOSS WILD-TYPE                        58   251
D64V13, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       6                 58
  WHITE                                          41                251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  44
  12P LOSS WILD-TYPE   5 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   44
  12P LOSS WILD-TYPE    5  304
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               44                304
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    50  18
  12Q LOSS WILD-TYPE 422 103
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                68                525 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                103 
$`12Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       43.76        45.60        34.65        36.53        30.44        23.61 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3552 
       20.28        61.84         9.63        26.01        33.99        13.02 
TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       50.04        31.07        17.03        24.03         2.01        50.99 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       32.02        33.04         2.96         5.79        22.42        16.44 
TCGA-AU-3779 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 
       14.50         2.14        12.20        49.08         8.02        29.06 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
        5.03         2.96        29.03        15.02        11.01        11.08 
TCGA-D5-6533 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 
        1.32         4.80        11.38        12.59         7.50        31.96 
TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-RU-A8FL TCGA-AF-2691 
       16.24        65.85        61.91        36.00        30.28        43.04 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-4021 
       14.50        15.39        34.03        29.98        48.03         3.98 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 
       23.01        15.95        38.56        10.19        13.97        10.98 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 
       24.13        51.48        17.00        16.31        16.41        28.57 
TCGA-F5-6812 TCGA-G5-6233 
        0.66        18.28 

$`12Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       37.02        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       19.66        16.24        24.92        56.25         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.20         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       55.04        85.48        63.62        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       11.90        70.03        24.13        39.48        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       19.10        34.49        37.74        10.39        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        20.98         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72        26.43         1.81         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02         5.03         8.98        15.02        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24       129.27        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.97         8.45         9.96        49.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.66               0.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             65.85             148.01 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             19.28              19.99 
[1] "0.7 - 65.8 (19.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    48  21
  12Q LOSS WILD-TYPE 398 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     48   21
  12Q LOSS WILD-TYPE  398  141
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON                48                398
  RECTUM               21                141
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q LOSS MUTATED        11        0        1        14         1         1
  12Q LOSS WILD-TYPE      93        1       35       159         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           1          4          9         11        9
  12Q LOSS WILD-TYPE        25         14         74         43       54
                    vv
clus                 STAGE IVA STAGE IVB
  12Q LOSS MUTATED           5         0
  12Q LOSS WILD-TYPE        21         2
D65V4, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  11                 93
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                14                159
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 1                 25
  STAGE IIIA                4                 14
  STAGE IIIB                9                 74
  STAGE IIIC               11                 43
  STAGE IV                  9                 54
  STAGE IVA                 5                 21
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     3  11  52   4
  12Q LOSS WILD-TYPE  17  95 365  63
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 17
  T2               11                 95
  T3               52                365
  T4                4                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12Q LOSS MUTATED    29  23  18
  12Q LOSS WILD-TYPE 316 127  97
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               29                316
  N1               23                127
  N2               18                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    44  14
  12Q LOSS WILD-TYPE 406  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     44   14
  12Q LOSS WILD-TYPE  406   74
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               44                406
  1               14                 74
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    32  38
  12Q LOSS WILD-TYPE 255 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     32   38
  12Q LOSS WILD-TYPE  255  287
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               32                255
  MALE                 38                287
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    55   3
  12Q LOSS WILD-TYPE 391  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     55    3
  12Q LOSS WILD-TYPE  391   25
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                55                391
  YES                3                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                     46                             2
  12Q LOSS WILD-TYPE                  336                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                      21                              0
  12Q LOSS WILD-TYPE                   125                             13
D65V10, multiclass
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         46                336
  COLON MUCINOUS ADENOCARCINOMA                 2                 58
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    52   0   4   3
  12Q LOSS WILD-TYPE 390   5  33  26
D65V11, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               52                390
  R1                0                  5
  R2                4                 33
  RX                3                 26
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     2
  12Q LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           4    45
  12Q LOSS WILD-TYPE                        60   247
D65V13, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 10
  BLACK OR AFRICAN AMERICAN                       4                 60
  WHITE                                          45                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"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  46
  12Q LOSS WILD-TYPE   5 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   46
  12Q LOSS WILD-TYPE    5  302
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               46                302
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   5
  13Q LOSS WILD-TYPE 459 116
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                575 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                116 
$`13Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-A01D TCGA-AZ-4681 TCGA-AZ-6607 
       23.01        18.05        24.00        10.98       106.75         3.19 
TCGA-CA-5797 TCGA-F4-6704 TCGA-G4-6314 TCGA-QG-A5Z1 TCGA-AG-3591 TCGA-AG-3594 
        3.29         1.55        35.93         8.42        34.03         2.01 
TCGA-AG-3600 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A020 TCGA-DC-6156 TCGA-DY-A0XA 
        6.05         3.98        23.01        10.98        15.02       126.44 

$`13Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        42.77        29.46        32.98        31.30        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       30.28        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       65.98        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
       11.01        15.02         5.03         8.98        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.55               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             148.01 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.00              20.02 
[1] "1.6 - 126.4 (13.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    12   8
  13Q LOSS WILD-TYPE 434 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    8
  13Q LOSS WILD-TYPE  434  154
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON                12                434
  RECTUM                8                154
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q LOSS MUTATED         3        0        0         6         0         0
  13Q LOSS WILD-TYPE     101        1       36       167        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1          0          1          4        3
  13Q LOSS WILD-TYPE        25         18         82         50       60
                    vv
clus                 STAGE IVA STAGE IVB
  13Q LOSS MUTATED           2         0
  13Q LOSS WILD-TYPE        24         2
D66V4, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  0                 36
  STAGE IIA                 6                167
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                0                 18
  STAGE IIIB                1                 82
  STAGE IIIC                4                 50
  STAGE IV                  3                 60
  STAGE IVA                 2                 24
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     1   2  14   3
  13Q LOSS WILD-TYPE  19 104 403  64
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                1                 19
  T2                2                104
  T3               14                403
  T4                3                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  13Q LOSS MUTATED     9   3   8
  13Q LOSS WILD-TYPE 336 147 107
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                9                336
  N1                3                147
  N2                8                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11   5
  13Q LOSS WILD-TYPE 439  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11    5
  13Q LOSS WILD-TYPE  439   83
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               11                439
  1                5                 83
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  11
  13Q LOSS WILD-TYPE 278 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE  278  314
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                278
  MALE                 11                314
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    13   2
  13Q LOSS WILD-TYPE 433  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     13    2
  13Q LOSS WILD-TYPE  433   26
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                13                433
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                      8                             3
  13Q LOSS WILD-TYPE                  374                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                       6                              2
  13Q LOSS WILD-TYPE                   140                             11
D66V10, multiclass
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          8                374
  COLON MUCINOUS ADENOCARCINOMA                 3                 57
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    16   0   1   1
  13Q LOSS WILD-TYPE 426   5  36  28
D66V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               16                426
  R1                0                  5
  R2                1                 36
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           1     7
  13Q LOSS WILD-TYPE                        63   285
D66V13, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       1                 63
  WHITE                                           7                285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  10
  13Q LOSS WILD-TYPE   5 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   10
  13Q LOSS WILD-TYPE    5  338
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               10                338
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   160  37
  14Q LOSS WILD-TYPE 312  84
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               197                396 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                 84 
$`14Q LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
        4.80        39.45        43.76        42.28        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       23.61        22.52        24.13        25.08        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 
       24.69        23.87        20.28        61.84         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       38.99         9.07        24.03        19.07        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       23.01        13.94        19.99         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 
       47.01        37.05        19.00        85.05        10.06        25.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       36.95        37.02        17.03        31.07        17.03        24.03 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       18.05        12.99        34.03        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O 
       34.06        26.01        24.00         7.96        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K 
       42.02        14.99        21.99         1.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 
       33.04        26.01         2.96         2.01        40.96         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
       22.42        27.42        16.44        14.50         0.95        33.01 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 
       17.85        18.84       109.28         1.41         5.65        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 
       29.56         5.23         1.61         3.06         2.14         0.07 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 
       12.20        49.08         1.91        25.02         8.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 
        2.96        29.03        13.02        15.02        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       45.40        12.26        56.09        18.25         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 
       14.30         4.80        11.38        38.20        13.32       140.38 
TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       14.04       119.93        31.96        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 
        0.53        28.21         8.35        82.39        61.91        91.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL 
       18.18        19.33        15.65        17.85        16.80        30.28 
TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 
       11.90        39.48        17.23        13.55        37.74        10.39 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       65.98        11.84        36.03        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3881 
       34.03        50.04         6.05         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        17.95        17.03        35.01         1.02        48.03 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       36.03        14.04        17.03         6.02        25.97        23.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
        1.94        38.96        38.04        38.56        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
       33.17         9.37         4.73        12.39         7.17        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
        5.03        13.97        27.95        10.98         4.01         5.03 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 
      129.27        51.48        20.55        17.00        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       16.41        10.78        11.97        31.30         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.76        18.28        55.76        26.43 

$`14Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       15.62        12.66         1.61         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 
       43.43        42.90        24.33        44.91        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.05        37.25        37.02        31.63        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        27.09         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.18        24.16        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       13.02         1.02        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        0.00        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       54.02         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
        0.99         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 
        2.01        20.98         2.01        13.05        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72        10.88         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        16.31        21.44        17.82        17.26        19.33 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
       75.95        58.39        32.94         5.13       106.75        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74         3.19        12.69         3.25         3.29        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32         9.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.03        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.41        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F 
        7.76       139.17         6.12        26.47        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 
       16.24        47.41        35.31       133.18        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       63.62        39.42        35.93        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV 
       79.69        10.98        19.33         9.93        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       29.46        32.98         8.42        31.30        21.90        70.03 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       24.13        43.04        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        86.63        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
        2.01        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99        20.98         7.99        29.98        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 
        0.99        19.99        36.95        13.02        14.01        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       13.94        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       49.97        61.97        41.00         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 
       26.43         1.81         6.97        78.12        21.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
        8.98        15.02        19.99         5.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        24.13        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
       19.96        20.91        18.28        15.85        17.69         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57         0.69         0.53         1.12        12.46        47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            140.38             148.01 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            19.040             20.035 
[1] "0.1 - 140.4 (19.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   136  66
  14Q LOSS WILD-TYPE 310  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    136   66
  14Q LOSS WILD-TYPE  310   96
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON               136                310
  RECTUM               66                 96
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q LOSS MUTATED        30        0        8        60         1         1
  14Q LOSS WILD-TYPE      74        1       28       113         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED          10          9         28         15       26
  14Q LOSS WILD-TYPE        16          9         55         39       37
                    vv
clus                 STAGE IVA STAGE IVB
  14Q LOSS MUTATED          12         0
  14Q LOSS WILD-TYPE        14         2
D67V4, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  30                 74
  STAGE IA                  0                  1
  STAGE II                  8                 28
  STAGE IIA                60                113
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                10                 16
  STAGE IIIA                9                  9
  STAGE IIIB               28                 55
  STAGE IIIC               15                 39
  STAGE IV                 26                 37
  STAGE IVA                12                 14
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED     9  31 145  19
  14Q LOSS WILD-TYPE  11  75 272  48
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                9                 11
  T2               31                 75
  T3              145                272
  T4               19                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  14Q LOSS MUTATED   105  63  36
  14Q LOSS WILD-TYPE 240  87  79
D67V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              105                240
  N1               63                 87
  N2               36                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   145  38
  14Q LOSS WILD-TYPE 305  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    145   38
  14Q LOSS WILD-TYPE  305   50
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              145                305
  1               38                 50
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    91 113
  14Q LOSS WILD-TYPE 196 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     91  113
  14Q LOSS WILD-TYPE  196  212
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               91                196
  MALE                113                212
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   153  14
  14Q LOSS WILD-TYPE 293  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    153   14
  14Q LOSS WILD-TYPE  293   14
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               153                293
  YES               14                 14
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                    130                             3
  14Q LOSS WILD-TYPE                  252                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                      64                              1
  14Q LOSS WILD-TYPE                    82                             12
D67V10, multiclass
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        130                252
  COLON MUCINOUS ADENOCARCINOMA                 3                 57
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   143   2  12  10
  14Q LOSS WILD-TYPE 299   3  25  19
D67V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              143                299
  R1                2                  3
  R2               12                 25
  RX               10                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     4
  14Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          22    96
  14Q LOSS WILD-TYPE                        42   196
D67V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      22                 42
  WHITE                                          96                196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2 114
  14Q LOSS WILD-TYPE   3 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2  114
  14Q LOSS WILD-TYPE    3  234
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              114                234
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   181  40
  15Q LOSS WILD-TYPE 291  81
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               221                372 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                40                 81 
$`15Q LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       24.33        44.91        45.60        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.45        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       20.61        21.76        20.28        61.84         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        1.02         6.97         9.07        37.05        29.00        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       33.99        21.01        13.02        23.01        19.99        19.99 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
        2.01        50.04        37.05        19.00        36.00        85.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        36.95        37.02        17.03        10.06        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
        0.99        31.07        17.03        24.03        29.98        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 
        2.01        21.99        50.99        13.05        34.06        24.00 
TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
        1.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 
       41.00         5.79        22.42        27.42        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 
        0.95        33.01        17.85        18.84       106.75        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 
       62.79        88.21        29.56         5.23         3.19         2.14 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 
       12.20        14.30       148.01        49.08         1.91        25.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       27.02        13.02        29.06         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 
        2.96        29.03        16.04        15.02        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       11.01        10.06        12.03        20.19         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         1.48         4.41         9.04         4.80 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.38       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
      131.51         6.12        95.18        31.96        47.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       16.24        33.67        13.25         0.53        47.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       65.85        55.04        63.62        61.91        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D 
       46.75        10.98        19.33        12.79        29.46        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
       30.28        11.90        24.13        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       14.50        10.39        65.98        32.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 
       24.00        46.03        34.03        34.03         6.05        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
       19.99        20.98        29.98         0.99        19.04        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
        0.69        10.19         6.05         9.37         7.17        21.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.03        13.97        27.95         4.01        41.36        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 
       24.13         0.49         2.40        15.85        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
       32.19         0.66         0.69        18.28        26.43 

$`15Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       15.62        12.66         9.53        46.65        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       35.11        13.94        37.05        37.25        37.02        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        24.13         8.38        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       24.92        56.25         9.63         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        26.01         0.99        14.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       24.00        17.95        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        14.93         0.00 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
        0.00        33.07         0.00        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       26.01        25.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
       27.02         0.99        21.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       10.88         0.20        16.44         0.46         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.26        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41         6.77        12.10       100.01        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         3.25         3.29         0.07        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04         8.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 
       32.02        15.02        15.02        15.02        12.00        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       13.05        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        43.27        17.85         4.80 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         3.68        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       38.20        49.91         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       35.74         6.18        34.42        41.42        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       28.21        82.39        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        85.48        39.42        35.93        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       18.18        19.33         9.93        15.65        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       42.77        32.98         8.42        31.30        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.23        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       14.01        48.03        32.02        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       46.03        20.98         6.02        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         1.45         0.72        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        12.39        78.12        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
        8.98        15.02        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
        5.29       126.44       129.27        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
        8.61        17.46         8.45         9.96        49.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        12.46        55.76        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            148.01             139.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            20.050             19.975 
[1] "0.5 - 148.0 (20.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   155  70
  15Q LOSS WILD-TYPE 291  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    155   70
  15Q LOSS WILD-TYPE  291   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON               155                291
  RECTUM               70                 92
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q LOSS MUTATED        33        0        7        59         3         2
  15Q LOSS WILD-TYPE      71        1       29       114         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8          9         31         26       32
  15Q LOSS WILD-TYPE        18          9         52         28       31
                    vv
clus                 STAGE IVA STAGE IVB
  15Q LOSS MUTATED          12         1
  15Q LOSS WILD-TYPE        14         1
D68V4, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  33                 71
  STAGE IA                  0                  1
  STAGE II                  7                 29
  STAGE IIA                59                114
  STAGE IIB                 3                  7
  STAGE IIC                 2                  1
  STAGE III                 8                 18
  STAGE IIIA                9                  9
  STAGE IIIB               31                 52
  STAGE IIIC               26                 28
  STAGE IV                 32                 31
  STAGE IVA                12                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED     9  32 164  23
  15Q LOSS WILD-TYPE  11  74 253  44
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                 11
  T2               32                 74
  T3              164                253
  T4               23                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  15Q LOSS MUTATED   112  66  50
  15Q LOSS WILD-TYPE 233  84  65
D68V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              112                233
  N1               66                 84
  N2               50                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   157  44
  15Q LOSS WILD-TYPE 293  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    157   44
  15Q LOSS WILD-TYPE  293   44
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              157                293
  1               44                 44
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   101 127
  15Q LOSS WILD-TYPE 186 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    101  127
  15Q LOSS WILD-TYPE  186  198
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              101                186
  MALE                127                198
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   166  15
  15Q LOSS WILD-TYPE 280  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    166   15
  15Q LOSS WILD-TYPE  280   13
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               166                280
  YES               15                 13
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                    141                            12
  15Q LOSS WILD-TYPE                  241                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                      64                              5
  15Q LOSS WILD-TYPE                    82                              8
D68V10, multiclass
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        141                241
  COLON MUCINOUS ADENOCARCINOMA                12                 48
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   163   2  15   9
  15Q LOSS WILD-TYPE 279   3  22  20
D68V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              163                279
  R1                2                  3
  R2               15                 22
  RX                9                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     3
  15Q LOSS WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          21   115
  15Q LOSS WILD-TYPE                        43   177
D68V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      21                 43
  WHITE                                         115                177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2 129
  15Q LOSS WILD-TYPE   3 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2  129
  15Q LOSS WILD-TYPE    3  219
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              129                219
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    30   9
  16P LOSS WILD-TYPE 442 112
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                39                554 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                112 
$`16P LOSS MUTATED`
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3685 TCGA-AA-3837 
       34.65        14.53        21.76        61.84        37.05        38.99 
TCGA-AA-3860 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       31.07         2.01        41.00        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 TCGA-CM-5863 
       16.31        17.85         5.65         3.19        22.03        15.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1D6 
       13.02        11.01        11.01        20.19        17.75        49.91 
TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL TCGA-T9-A92H TCGA-AG-3578 
        7.50        18.18        10.98        30.28        11.90        32.02 
TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-4005 TCGA-DC-6682 
       34.03         6.05        19.99        19.04        14.04         4.01 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
       32.19         0.53        18.28 

$`16P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       27.42        10.88         0.20         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        75.95        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.61        12.69         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
        2.01        50.04        12.03         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         1.12         0.76        12.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.46               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             61.84             148.01 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             17.75              20.20 
[1] "0.5 - 61.8 (17.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31  10
  16P LOSS WILD-TYPE 415 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31   10
  16P LOSS WILD-TYPE  415  152
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON                31                415
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P LOSS MUTATED         3        0        1        17         0         1
  16P LOSS WILD-TYPE     101        1       35       156        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0          0          6          6        3
  16P LOSS WILD-TYPE        26         18         77         48       60
                    vv
clus                 STAGE IVA STAGE IVB
  16P LOSS MUTATED           4         0
  16P LOSS WILD-TYPE        22         2
D69V4, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                17                156
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 0                 26
  STAGE IIIA                0                 18
  STAGE IIIB                6                 77
  STAGE IIIC                6                 48
  STAGE IV                  3                 60
  STAGE IVA                 4                 22
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   4  32   5
  16P LOSS WILD-TYPE  20 102 385  62
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                 20
  T2                4                102
  T3               32                385
  T4                5                 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
  16P LOSS MUTATED    22   8  11
  16P LOSS WILD-TYPE 323 142 104
D69V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               22                323
  N1                8                142
  N2               11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    28   7
  16P LOSS WILD-TYPE 422  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     28    7
  16P LOSS WILD-TYPE  422   81
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               28                422
  1                7                 81
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    21  20
  16P LOSS WILD-TYPE 266 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     21   20
  16P LOSS WILD-TYPE  266  305
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               21                266
  MALE                 20                305
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31   2
  16P LOSS WILD-TYPE 415  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31    2
  16P LOSS WILD-TYPE  415   26
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                31                415
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                     25                             6
  16P LOSS WILD-TYPE                  357                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                       8                              1
  16P LOSS WILD-TYPE                   138                             12
D69V10, multiclass
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         25                357
  COLON MUCINOUS ADENOCARCINOMA                 6                 54
  RECTAL ADENOCARCINOMA                         8                138
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    30   1   0   1
  16P LOSS WILD-TYPE 412   4  37  28
D69V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               30                412
  R1                1                  4
  R2                0                 37
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           9    21
  16P LOSS WILD-TYPE                        55   271
D69V13, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       9                 55
  WHITE                                          21                271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  28
  16P LOSS WILD-TYPE   4 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   28
  16P LOSS WILD-TYPE    4  320
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               28                320
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    34   7
  16Q LOSS WILD-TYPE 438 114
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                552 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                114 
$`16Q LOSS MUTATED`
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-6651 TCGA-AA-3494 TCGA-AA-3685 
       34.65        14.53        29.19        21.76         1.02        37.05 
TCGA-AA-3837 TCGA-AA-3860 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK TCGA-AY-4070 
       38.99        31.07         2.01        41.00        16.44        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-6169 
       17.85         5.65         3.19        22.03        15.02        13.02 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1DA TCGA-NH-A50T 
       11.01        11.01        20.19        17.75         7.50        18.18 
TCGA-NH-A50U TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3591 
       10.98        30.28        11.90        10.39        32.02        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
        6.05        19.99         7.99        32.98        19.04         1.02 
TCGA-AG-4005 TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
       14.04         4.01        32.19         0.53        18.28 

$`16Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        79.69        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        21.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       10.39        14.50        16.83        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       13.94        19.99        20.98         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       19.99        28.04        36.03         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57         0.39         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.53               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             41.00             148.01 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.44              20.35 
[1] "0.5 - 41.0 (16.4)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    29  14
  16Q LOSS WILD-TYPE 417 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     29   14
  16Q LOSS WILD-TYPE  417  148
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON                29                417
  RECTUM               14                148
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q LOSS MUTATED         6        0        1        15         0         1
  16Q LOSS WILD-TYPE      98        1       35       158        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           0          0          6          7        4
  16Q LOSS WILD-TYPE        26         18         77         47       59
                    vv
clus                 STAGE IVA STAGE IVB
  16Q LOSS MUTATED           3         0
  16Q LOSS WILD-TYPE        23         2
D70V4, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   6                 98
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                15                158
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 0                 26
  STAGE IIIA                0                 18
  STAGE IIIB                6                 77
  STAGE IIIC                7                 47
  STAGE IV                  4                 59
  STAGE IVA                 3                 23
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     0   7  31   5
  16Q LOSS WILD-TYPE  20  99 386  62
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                 20
  T2                7                 99
  T3               31                386
  T4                5                 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
  16Q LOSS MUTATED    24   7  12
  16Q LOSS WILD-TYPE 321 143 103
D70V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               24                321
  N1                7                143
  N2               12                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    30   6
  16Q LOSS WILD-TYPE 420  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     30    6
  16Q LOSS WILD-TYPE  420   82
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               30                420
  1                6                 82
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  22
  16Q LOSS WILD-TYPE 266 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   22
  16Q LOSS WILD-TYPE  266  303
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                266
  MALE                 22                303
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    32   3
  16Q LOSS WILD-TYPE 414  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     32    3
  16Q LOSS WILD-TYPE  414   25
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                32                414
  YES                3                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                     24                             5
  16Q LOSS WILD-TYPE                  358                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                      12                              1
  16Q LOSS WILD-TYPE                   134                             12
D70V10, multiclass
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         24                358
  COLON MUCINOUS ADENOCARCINOMA                 5                 55
  RECTAL ADENOCARCINOMA                        12                134
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    31   1   1   1
  16Q LOSS WILD-TYPE 411   4  36  28
D70V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               31                411
  R1                1                  4
  R2                1                 36
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           9    19
  16Q LOSS WILD-TYPE                        55   273
D70V13, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       9                 55
  WHITE                                          19                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  27
  16Q LOSS WILD-TYPE   4 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   27
  16Q LOSS WILD-TYPE    4  321
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               27                321
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   255  72
  17P LOSS WILD-TYPE 217  49
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               327                266 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                72                 49 
$`17P LOSS MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        1.61        39.45        43.76        43.76        43.43        24.33 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5666 
       14.53        32.45        32.91        31.63        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6649 
       29.16        27.09        22.52        24.13        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       20.61        23.87        20.28        61.84         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
       24.03        37.05        36.03        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       36.00        85.05        10.06        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       37.02        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01T 
       15.02        10.98        32.02        12.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       37.02         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42         0.20        16.44         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
        0.95        33.01        17.85       109.28         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13       106.75        22.36        65.00        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23         3.19         1.61        12.69         2.14 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        3.29        12.20        14.30        49.08         9.99         1.91 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 
       25.02         8.02        27.02        13.02        29.06         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       15.02        17.03        29.03        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       15.02        11.01        13.05        11.08        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        1.32        43.27        17.13        12.49        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A0XD 
        4.41        12.43        14.30         9.04        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       131.51       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 
      119.93        35.97       117.07        31.96        11.11        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6303 
       16.24        33.67        13.25         8.35        23.51        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        63.62        39.42        35.93        61.91 
TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       26.43        91.79        46.75        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       15.65        12.79        17.85        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 
        8.42        21.90        30.28        11.90        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       15.39        20.02        86.63        65.98        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 
       32.02         7.07        36.03        24.00        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 
        2.01        50.04         0.99        13.94        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 
        0.99        37.02        32.98         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.95        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A008 
       28.04        36.03        14.04        17.03         3.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        15.95         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       12.00        31.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 
       41.00        38.56         0.69         0.72        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 
       33.17         6.97        12.39         7.17        11.01        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        19.99         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         0.49         2.40 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       16.41        11.51        10.78        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 
       49.51        31.30        28.57         0.39         0.69         0.53 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.76        12.46        55.76 

$`17P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       15.62         4.80        12.66         9.53        46.65        42.90 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 
       44.91        45.60        13.94        37.02        36.53        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       33.53        23.61        22.09        22.06         8.38        25.08 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.69        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       24.92        56.25         9.63         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 
       63.98         1.02        13.02         1.02         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        15.02        11.01         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       14.93         0.00        17.03         0.00         0.00        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       24.00         2.01        21.99        13.05        34.06        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I 
       18.05         4.01         0.99        34.98         1.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
        0.07        56.55         0.72        10.88         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 
       21.44        17.82        17.26        19.33        18.84        75.95 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39        32.94        62.79        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       11.74         3.06         3.25         0.07        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 
       15.02        15.02        12.00         2.96        16.04        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 
       14.04        12.95        11.08        11.01        12.03        20.19 
TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       20.42        15.12        17.85         4.80        16.14         3.68 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
      119.70        49.91         7.50       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
       60.79        98.24        95.18         8.61        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 
        6.18        47.87         1.55        41.42         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       53.62        85.48        36.00        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        18.18        19.33 
TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 
       29.46        31.30        70.03        24.13        10.39        16.83 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39        36.03         8.02        20.05         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       34.03        12.03         6.05        15.95        19.99        19.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       29.98         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 
       14.01         1.02        46.03        20.98        36.03         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       10.98        49.97        38.96        61.97        38.04         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
       26.43         1.81         9.37         4.73        78.12        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02         5.03         8.98        15.02        27.95         5.95 
TCGA-DC-6682 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 
        4.01        32.61        20.55        19.96        15.85         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 
       13.64        17.46        32.19         0.66         1.12        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            140.38             148.01 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            19.990             20.005 
[1] "0.2 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   232 102
  17P LOSS WILD-TYPE 214  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    232  102
  17P LOSS WILD-TYPE  214   60
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON               232                214
  RECTUM              102                 60
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P LOSS MUTATED        46        0       18        86         3         2
  17P LOSS WILD-TYPE      58        1       18        87         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          14         14         47         36       44
  17P LOSS WILD-TYPE        12          4         36         18       19
                    vv
clus                 STAGE IVA STAGE IVB
  17P LOSS MUTATED          18         2
  17P LOSS WILD-TYPE         8         0
D71V4, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  46                 58
  STAGE IA                  0                  1
  STAGE II                 18                 18
  STAGE IIA                86                 87
  STAGE IIB                 3                  7
  STAGE IIC                 2                  1
  STAGE III                14                 12
  STAGE IIIA               14                  4
  STAGE IIIB               47                 36
  STAGE IIIC               36                 18
  STAGE IV                 44                 19
  STAGE IVA                18                  8
  STAGE IVB                 2                  0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED     9  53 237  39
  17P LOSS WILD-TYPE  11  53 180  28
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                9                 11
  T2               53                 53
  T3              237                180
  T4               39                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17P LOSS MUTATED   169  94  74
  17P LOSS WILD-TYPE 176  56  41
D71V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              169                176
  N1               94                 56
  N2               74                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   238  62
  17P LOSS WILD-TYPE 212  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    238   62
  17P LOSS WILD-TYPE  212   26
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              238                212
  1               62                 26
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   150 188
  17P LOSS WILD-TYPE 137 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    150  188
  17P LOSS WILD-TYPE  137  137
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              150                137
  MALE                188                137
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   247  15
  17P LOSS WILD-TYPE 199  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    247   15
  17P LOSS WILD-TYPE  199   13
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               247                199
  YES               15                 13
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                    215                            14
  17P LOSS WILD-TYPE                  167                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                      95                              6
  17P LOSS WILD-TYPE                    51                              7
D71V10, multiclass
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        215                167
  COLON MUCINOUS ADENOCARCINOMA                14                 46
  RECTAL ADENOCARCINOMA                        95                 51
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   237   3  25  11
  17P LOSS WILD-TYPE 205   2  12  18
D71V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              237                205
  R1                3                  2
  R2               25                 12
  RX               11                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     6
  17P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          33   165
  17P LOSS WILD-TYPE                        31   127
D71V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      33                 31
  WHITE                                         165                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3 190
  17P LOSS WILD-TYPE   2 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3  190
  17P LOSS WILD-TYPE    2  158
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              190                158
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    72  22
  17Q LOSS WILD-TYPE 400  99
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                94                499 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                 99 
$`17Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5666 TCGA-A6-6649 
       43.76        43.76        37.05        32.45        32.71        24.16 
TCGA-AA-3495 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 TCGA-AA-3662 
       37.05        24.03        12.99        21.01        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3869 
        2.01        50.04        37.05        10.06        37.02        27.02 
TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       24.00        26.01        27.02         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       10.98        32.02        33.04        37.02         2.96        39.98 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-A69D 
       41.00         5.79        22.42         0.20        14.50        17.85 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 
       12.10         3.29        12.20        49.08        27.02        13.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6924 
        5.03        15.02        45.40        43.27        12.49        14.30 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6704 
       11.38        38.20        12.59       140.38        31.96         1.55 
TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6314 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A6GB 
       13.25         8.35        35.93        26.43        10.98        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QL-A97D TCGA-AF-4110 
       12.79        17.85        42.77        32.98        21.90        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3611 TCGA-AG-3896 
       15.39        65.98        36.03        34.03        13.94         1.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A023 
       32.02        28.04        13.94        25.97        12.00        51.98 
TCGA-AG-A02X TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 
       41.00        10.19        13.97        10.98         5.03         5.29 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 
       24.13         0.49         2.40        17.69        16.41        11.51 
TCGA-F5-6702 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 
       28.57         0.53         0.76        55.76 

$`17Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 
       29.19        33.53        23.61        22.09        22.06        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3496 
        9.63         5.03         7.04         3.02         1.02         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H 
        1.02        35.01        26.01        39.06        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        10.88        16.44         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.14         3.25         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 
       20.02        37.02        25.02        26.04         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       20.19        20.42        17.75        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        47.41        35.31       133.18        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        79.69        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        9.93        16.80        29.46         8.42        31.30        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       13.55        19.10        34.49        37.74        10.39        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 
        6.05         0.99        15.95        19.99        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 
       17.03        13.02        35.01        14.01        48.03        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        1.45         0.69         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA 
       15.02        27.95        19.99         5.95         4.01       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24       129.27        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        31.30         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.66         0.69         1.12        12.46        18.28        47.08 
TCGA-G5-6641 
       26.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            140.38             148.01 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             20.50              19.99 
[1] "0.2 - 140.4 (20.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    67  28
  17Q LOSS WILD-TYPE 379 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     67   28
  17Q LOSS WILD-TYPE  379  134
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON                67                379
  RECTUM               28                134
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q LOSS MUTATED        12        0        6        18         1         2
  17Q LOSS WILD-TYPE      92        1       30       155         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4          5         14         13       11
  17Q LOSS WILD-TYPE        22         13         69         41       52
                    vv
clus                 STAGE IVA STAGE IVB
  17Q LOSS MUTATED           6         1
  17Q LOSS WILD-TYPE        20         1
D72V4, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  12                 92
  STAGE IA                  0                  1
  STAGE II                  6                 30
  STAGE IIA                18                155
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 4                 22
  STAGE IIIA                5                 13
  STAGE IIIB               14                 69
  STAGE IIIC               13                 41
  STAGE IV                 11                 52
  STAGE IVA                 6                 20
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED     0  16  65  15
  17Q LOSS WILD-TYPE  20  90 352  52
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                 20
  T2               16                 90
  T3               65                352
  T4               15                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17Q LOSS MUTATED    41  32  23
  17Q LOSS WILD-TYPE 304 118  92
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               41                304
  N1               32                118
  N2               23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    60  17
  17Q LOSS WILD-TYPE 390  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     60   17
  17Q LOSS WILD-TYPE  390   71
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               60                390
  1               17                 71
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    42  54
  17Q LOSS WILD-TYPE 245 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     42   54
  17Q LOSS WILD-TYPE  245  271
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               42                245
  MALE                 54                271
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    71   6
  17Q LOSS WILD-TYPE 375  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     71    6
  17Q LOSS WILD-TYPE  375   22
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                71                375
  YES                6                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                     58                             8
  17Q LOSS WILD-TYPE                  324                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                      26                              2
  17Q LOSS WILD-TYPE                   120                             11
D72V10, multiclass
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         58                324
  COLON MUCINOUS ADENOCARCINOMA                 8                 52
  RECTAL ADENOCARCINOMA                        26                120
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    68   1   7   6
  17Q LOSS WILD-TYPE 374   4  30  23
D72V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               68                374
  R1                1                  4
  R2                7                 30
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1     3
  17Q LOSS WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          11    45
  17Q LOSS WILD-TYPE                        53   247
D72V13, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      11                 53
  WHITE                                          45                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"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  55
  17Q LOSS WILD-TYPE   5 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   55
  17Q LOSS WILD-TYPE    5  293
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               55                293
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   297  70
  18P LOSS WILD-TYPE 175  51
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               367                226 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                 51 
$`18P LOSS MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        32.71        29.16        27.09        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       37.05         1.02         6.97        38.99         9.07        37.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       14.01        33.99        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       12.99        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
        7.96        19.00        34.03        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       14.99        21.99         1.02        15.02        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        26.01         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        5.03        41.00        40.96        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
       22.42        27.42         0.20        16.44        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       33.01        17.26        17.85        18.84       109.28         5.65 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 
        5.13       106.75        22.36        65.00        62.79        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       29.56         5.23         1.61        12.69         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.07        12.20        14.30        49.08         9.99         1.91 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       25.02         8.02        13.02        29.06        22.03        30.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 
       21.99        13.02        15.02        11.01        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25         1.32        17.85        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        1.48        12.43        14.30         9.04         4.80        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      140.38        44.32       131.51       139.17        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        35.74         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       33.67        13.25         0.53        47.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 
       82.39        23.51        65.85        55.04        63.62        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       61.91        36.00        46.75        74.79        18.18        10.98 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        30.28        11.90        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        34.49        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       12.00         7.07        36.03        20.05        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        34.03        50.04         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
       13.94        19.99        20.98         7.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 
       36.03         1.02        17.03         3.98        46.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        70.03        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76        12.46        18.28        55.76 
TCGA-G5-6641 
       26.43 

$`18P LOSS WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 
        9.53        46.65        42.90        37.02        31.63        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6653 
       22.06        22.52         8.38        25.08        24.16        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       58.03        63.98         1.02        13.02         1.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3549 
       36.03         8.05         0.00        29.00         0.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
        2.01         2.01        25.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       17.03        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        37.02        39.06        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72        10.88         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       16.31        21.44        17.82        19.33        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        1.41        32.94        88.21        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       11.74         3.19         3.06         3.25        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       26.04        27.02        22.98        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       13.05        11.08        19.59        20.42        17.75        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       15.12         4.80        16.14        15.58         3.68         4.41 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A28C 
       92.75         7.50       135.65         7.76         6.12        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 
       60.79        98.24        35.74         6.18        47.87        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       39.42        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        91.79        79.69        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 
       15.65        29.46        31.30        70.03        19.10        16.83 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 
       10.39        32.02         8.02         1.02         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 
        6.05        19.99         0.99         0.99        19.04        17.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A01Y 
       13.02        14.01        14.04        20.98        36.03        64.01 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
       49.97        38.96        61.97         1.45         1.81         5.29 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       32.61        19.96        20.91         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
        9.96         0.53         1.12        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.38             148.01 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             20.28              19.33 
[1] "0.1 - 140.4 (20.3)" "0.0 - 148.0 (19.3)"
[1] "hr=" "1.1"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   248 126
  18P LOSS WILD-TYPE 198  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    248  126
  18P LOSS WILD-TYPE  198   36
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON               248                198
  RECTUM              126                 36
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P LOSS MUTATED        57        0       16        99         4         3
  18P LOSS WILD-TYPE      47        1       20        74         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          11         13         56         36       50
  18P LOSS WILD-TYPE        15          5         27         18       13
                    vv
clus                 STAGE IVA STAGE IVB
  18P LOSS MUTATED          23         1
  18P LOSS WILD-TYPE         3         1
D73V4, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  57                 47
  STAGE IA                  0                  1
  STAGE II                 16                 20
  STAGE IIA                99                 74
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                11                 15
  STAGE IIIA               13                  5
  STAGE IIIB               56                 27
  STAGE IIIC               36                 18
  STAGE IV                 50                 13
  STAGE IVA                23                  3
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    12  61 263  41
  18P LOSS WILD-TYPE   8  45 154  26
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               12                  8
  T2               61                 45
  T3              263                154
  T4               41                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18P LOSS MUTATED   193 105  78
  18P LOSS WILD-TYPE 152  45  37
D73V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              193                152
  N1              105                 45
  N2               78                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   263  73
  18P LOSS WILD-TYPE 187  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    263   73
  18P LOSS WILD-TYPE  187   15
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              263                187
  1               73                 15
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   172 205
  18P LOSS WILD-TYPE 115 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    172  205
  18P LOSS WILD-TYPE  115  120
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              172                115
  MALE                205                120
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   274  20
  18P LOSS WILD-TYPE 172   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    274   20
  18P LOSS WILD-TYPE  172    8
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               274                172
  YES               20                  8
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                    234                            11
  18P LOSS WILD-TYPE                  148                            49
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                     119                              7
  18P LOSS WILD-TYPE                    27                              6
D73V10, multiclass
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        234                148
  COLON MUCINOUS ADENOCARCINOMA                11                 49
  RECTAL ADENOCARCINOMA                       119                 27
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   269   2  29  14
  18P LOSS WILD-TYPE 173   3   8  15
D73V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              269                173
  R1                2                  3
  R2               29                  8
  RX               14                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  1     6
  18P LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          40   184
  18P LOSS WILD-TYPE                        24   108
D73V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      40                 24
  WHITE                                         184                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"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4 215
  18P LOSS WILD-TYPE   1 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  215
  18P LOSS WILD-TYPE    1  133
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              215                133
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   318  79
  18Q LOSS WILD-TYPE 154  42
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               397                196 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                79                 42 
$`18Q LOSS MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       27.09        24.13        25.18        20.61        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01        12.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.05         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 
       15.02        37.05        19.00        36.00        85.05        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       33.07         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 
       27.02        29.98        18.05        12.99        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       34.06        26.01        24.00        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       34.03        42.02        17.03        14.99        21.99         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        10.98        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        40.96        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42         0.20        16.44         0.46        14.50        16.31 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       33.01        17.26        17.85        18.84       109.28         5.65 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         1.61        12.69         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 
        3.29         0.07        12.20        14.30       148.01        49.08 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
        9.99         1.91        25.02         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
        2.96        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25         1.32        17.85        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        1.48        12.43        14.30         9.04         4.80        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M 
        6.12        14.04        26.47       119.93       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        11.11        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 
       41.42        16.24        13.25         0.53        47.41        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        8.35        82.39        23.51        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       63.62        39.42        35.93        61.91        36.00        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       46.75        74.79        18.18        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        30.28        11.90        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       14.50        15.39        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       50.04         6.05         0.99        15.95        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
       38.56         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.41        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`18Q LOSS WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 
        9.53        46.65        42.90        33.53        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        24.16        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       19.66        16.24        24.92         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3529 
       63.98         1.02        13.02         1.02         8.05         0.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       29.00         0.99        21.01        17.95        29.95        20.98 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
        6.97        54.02         0.92        47.05        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
        0.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00        36.03        32.05        53.00        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 
       33.01        26.01        24.00         2.01        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       38.04         4.01        27.02         0.99        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       31.00        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       21.37        56.55         0.72        10.88         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        21.44        17.82        19.33        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
        1.41        32.94        49.41         6.77       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.19         3.06         3.25        12.76        10.06        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 
      124.27        23.05        20.02        37.02        26.04        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       32.02        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 
       12.99        14.04        12.95        13.05        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 
       43.27        15.12         4.80        16.14         3.68         4.41 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      135.65         7.76        81.37        35.97        60.79        98.24 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 
       35.74         6.18        47.87        33.67        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 
       74.56        67.30        53.62        85.48        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       26.04        13.78        35.80        26.17        79.69        19.33 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AF-6672 
       15.65        29.46        31.30        70.03        16.83        10.39 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3885 
        8.02         1.02        12.03        19.99         0.99        17.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N 
       13.02        14.01        20.98        36.03        49.97        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 
        1.45         1.81         5.29        32.61        19.96         8.61 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       17.46         9.96         0.53         1.12 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            148.01             135.65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             20.02              19.81 
[1] "0.1 - 148.0 (20.0)" "0.0 - 135.7 (19.8)"
[1] "hr=" "1.1"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   267 137
  18Q LOSS WILD-TYPE 179  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    267  137
  18Q LOSS WILD-TYPE  179   25
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON               267                179
  RECTUM              137                 25
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q LOSS MUTATED        58        0       20       106         4         3
  18Q LOSS WILD-TYPE      46        1       16        67         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          14         14         60         41       53
  18Q LOSS WILD-TYPE        12          4         23         13       10
                    vv
clus                 STAGE IVA STAGE IVB
  18Q LOSS MUTATED          24         1
  18Q LOSS WILD-TYPE         2         1
D74V4, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  58                 46
  STAGE IA                  0                  1
  STAGE II                 20                 16
  STAGE IIA               106                 67
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                14                 12
  STAGE IIIA               14                  4
  STAGE IIIB               60                 23
  STAGE IIIC               41                 13
  STAGE IV                 53                 10
  STAGE IVA                24                  2
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    11  65 286  44
  18Q LOSS WILD-TYPE   9  41 131  23
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               11                  9
  T2               65                 41
  T3              286                131
  T4               44                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18Q LOSS MUTATED   204 113  88
  18Q LOSS WILD-TYPE 141  37  27
D74V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              204                141
  N1              113                 37
  N2               88                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   287  76
  18Q LOSS WILD-TYPE 163  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    287   76
  18Q LOSS WILD-TYPE  163   12
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              287                163
  1               76                 12
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   185 222
  18Q LOSS WILD-TYPE 102 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    185  222
  18Q LOSS WILD-TYPE  102  103
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              185                102
  MALE                222                103
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   297  21
  18Q LOSS WILD-TYPE 149   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    297   21
  18Q LOSS WILD-TYPE  149    7
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               297                149
  YES               21                  7
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                    250                            14
  18Q LOSS WILD-TYPE                  132                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                     126                             10
  18Q LOSS WILD-TYPE                    20                              3
D74V10, multiclass
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        250                132
  COLON MUCINOUS ADENOCARCINOMA                14                 46
  RECTAL ADENOCARCINOMA                       126                 20
  RECTAL MUCINOUS ADENOCARCINOMA               10                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   292   3  30  14
  18Q LOSS WILD-TYPE 150   2   7  15
D74V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              292                150
  R1                3                  2
  R2               30                  7
  RX               14                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  1     6
  18Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          43   199
  18Q LOSS WILD-TYPE                        21    93
D74V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      43                 21
  WHITE                                         199                 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"
D74V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 233
  18Q LOSS WILD-TYPE   1 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  233
  18Q LOSS WILD-TYPE    1  115
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              233                115
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    43  16
  19P LOSS WILD-TYPE 429 105
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                534 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                105 
$`19P LOSS MUTATED`
TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3538 TCGA-AA-3552 
       34.65        25.08        61.84        58.03        26.01        13.02 
TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3866 TCGA-AA-3867 
       23.01        19.99         2.01        36.00        17.03        24.03 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T 
       24.00         2.01         2.01        10.98        12.00        33.04 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6965 TCGA-AZ-4616 TCGA-AZ-4684 
       26.01        39.98        41.00         0.20         5.13        65.00 
TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-6533 
        3.29       148.01        49.08        13.05        45.40         1.32 
TCGA-D5-6537 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6317 
        4.80        44.32         6.12        33.67         8.35        36.00 
TCGA-NH-A50U TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 TCGA-AG-3725 
       10.98        30.28        24.13        14.50        15.95        20.98 
TCGA-AG-3881 TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6624 TCGA-DC-5869 
       19.04        17.03         9.07        64.01         4.73         5.03 
TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 
       13.97        24.13        51.48         0.49        16.34        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       13.64        11.97        31.30        28.57        18.28 

$`19P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        37.02        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
        3.02         1.02        37.05         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        31.07        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        15.02        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      133.18        28.21        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        61.91        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       79.69        18.18        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        11.90        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       65.98        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95        36.03         1.02        12.00        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         8.98        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       16.41         8.61        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.2                0.0 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            148.01             140.38 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            19.040             20.005 
[1] "0.2 - 148.0 (19.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    40  22
  19P LOSS WILD-TYPE 406 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     40   22
  19P LOSS WILD-TYPE  406  140
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON                40                406
  RECTUM               22                140
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P LOSS MUTATED         8        0        2        10         1         2
  19P LOSS WILD-TYPE      96        1       34       163         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           5          1          6          9       10
  19P LOSS WILD-TYPE        21         17         77         45       53
                    vv
clus                 STAGE IVA STAGE IVB
  19P LOSS MUTATED           7         1
  19P LOSS WILD-TYPE        19         1
D75V4, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   8                 96
  STAGE IA                  0                  1
  STAGE II                  2                 34
  STAGE IIA                10                163
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 5                 21
  STAGE IIIA                1                 17
  STAGE IIIB                6                 77
  STAGE IIIC                9                 45
  STAGE IV                 10                 53
  STAGE IVA                 7                 19
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     1   9  45   8
  19P LOSS WILD-TYPE  19  97 372  59
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 19
  T2                9                 97
  T3               45                372
  T4                8                 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
  19P LOSS MUTATED    23  16  24
  19P LOSS WILD-TYPE 322 134  91
D75V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               23                322
  N1               16                134
  N2               24                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    38  17
  19P LOSS WILD-TYPE 412  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     38   17
  19P LOSS WILD-TYPE  412   71
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               38                412
  1               17                 71
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    30  33
  19P LOSS WILD-TYPE 257 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     30   33
  19P LOSS WILD-TYPE  257  292
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               30                257
  MALE                 33                292
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    44   2
  19P LOSS WILD-TYPE 402  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     44    2
  19P LOSS WILD-TYPE  402   26
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                44                402
  YES                2                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                     32                             7
  19P LOSS WILD-TYPE                  350                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                      21                              0
  19P LOSS WILD-TYPE                   125                             13
D75V10, multiclass
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         32                350
  COLON MUCINOUS ADENOCARCINOMA                 7                 53
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    41   0   6   3
  19P LOSS WILD-TYPE 401   5  31  26
D75V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               41                401
  R1                0                  5
  R2                6                 31
  RX                3                 26
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           5    30
  19P LOSS WILD-TYPE                        59   262
D75V13, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       5                 59
  WHITE                                          30                262
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  34
  19P LOSS WILD-TYPE   5 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   34
  19P LOSS WILD-TYPE    5  314
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               34                314
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    42  12
  19Q LOSS WILD-TYPE 430 109
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                539 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                109 
$`19Q LOSS MUTATED`
TCGA-A6-3807 TCGA-AA-3538 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3692 
       34.65        26.01        23.01        19.99         2.01        36.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-A004 
       17.03        24.03        24.00         2.01         2.01        13.94 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W 
       21.99        10.98        33.04        26.01        39.98        41.00 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6675 
        5.13        65.00         3.29       148.01        49.08        13.05 
TCGA-D5-5537 TCGA-D5-6533 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6704 TCGA-F4-6808 
       45.40         1.32        44.32         6.12         1.55        33.67 
TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-4110 
        8.35        36.00        10.98        30.28        24.13        14.50 
TCGA-AG-3591 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3881 TCGA-AG-4001 TCGA-AG-A011 
       34.03        15.95        20.98        19.04        36.03        37.02 
TCGA-AG-A01Y TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-5869 TCGA-DY-A1DF TCGA-EF-5830 
       64.01         4.73        21.01         5.03        24.13         0.49 
TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       16.34        11.51        11.97        31.30        28.57        18.28 

$`19Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        37.02        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
        2.01        12.99        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98         1.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
        1.02        35.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       61.91        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        11.90        70.03        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       13.55        19.10        34.49        37.74        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       13.94        19.99         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        70.03        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.05        33.17         6.97         9.37        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
        7.17        11.01        15.02         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.31        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        55.76        47.08        26.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            148.01             140.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             21.50              19.99 
[1] "0.5 - 148.0 (21.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    35  19
  19Q LOSS WILD-TYPE 411 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     35   19
  19Q LOSS WILD-TYPE  411  143
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON                35                411
  RECTUM               19                143
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q LOSS MUTATED         7        0        2        12         1         2
  19Q LOSS WILD-TYPE      97        1       34       161         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           5          0          5          8        7
  19Q LOSS WILD-TYPE        21         18         78         46       56
                    vv
clus                 STAGE IVA STAGE IVB
  19Q LOSS MUTATED           5         1
  19Q LOSS WILD-TYPE        21         1
D76V4, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   7                 97
  STAGE IA                  0                  1
  STAGE II                  2                 34
  STAGE IIA                12                161
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 5                 21
  STAGE IIIA                0                 18
  STAGE IIIB                5                 78
  STAGE IIIC                8                 46
  STAGE IV                  7                 56
  STAGE IVA                 5                 21
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     1   7  41   6
  19Q LOSS WILD-TYPE  19  99 376  61
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 19
  T2                7                 99
  T3               41                376
  T4                6                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19Q LOSS MUTATED    24  10  21
  19Q LOSS WILD-TYPE 321 140  94
D76V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               24                321
  N1               10                140
  N2               21                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    37  12
  19Q LOSS WILD-TYPE 413  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     37   12
  19Q LOSS WILD-TYPE  413   76
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               37                413
  1               12                 76
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29  26
  19Q LOSS WILD-TYPE 258 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   26
  19Q LOSS WILD-TYPE  258  299
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               29                258
  MALE                 26                299
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    39   3
  19Q LOSS WILD-TYPE 407  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     39    3
  19Q LOSS WILD-TYPE  407   25
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                39                407
  YES                3                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                     28                             6
  19Q LOSS WILD-TYPE                  354                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                      18                              0
  19Q LOSS WILD-TYPE                   128                             13
D76V10, multiclass
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         28                354
  COLON MUCINOUS ADENOCARCINOMA                 6                 54
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    39   0   4   3
  19Q LOSS WILD-TYPE 403   5  33  26
D76V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               39                403
  R1                0                  5
  R2                4                 33
  RX                3                 26
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  1     1
  19Q LOSS WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4    24
  19Q LOSS WILD-TYPE                        60   268
D76V13, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 11
  BLACK OR AFRICAN AMERICAN                       4                 60
  WHITE                                          24                268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  30
  19Q LOSS WILD-TYPE   5 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   30
  19Q LOSS WILD-TYPE    5  318
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               30                318
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    54  10
  20P LOSS WILD-TYPE 418 111
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                64                529 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                111 
$`20P LOSS MUTATED`
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 
       32.71        29.16        24.13        38.99         9.07        26.01 
TCGA-AA-3553 TCGA-AA-3681 TCGA-AA-3841 TCGA-AA-3855 TCGA-AA-3867 TCGA-AA-3952 
       24.00         5.98        36.95        32.05        24.03         2.01 
TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01Z TCGA-AA-A03J 
        2.01        19.00        34.03        42.02        37.02        40.96 
TCGA-AZ-4308 TCGA-AZ-6606 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 
      109.28        11.74         9.99         1.91        22.03        30.08 
TCGA-CM-6168 TCGA-CM-6170 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6923 
       12.99        15.02        56.09        55.92        43.27        12.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
       92.75        49.91        13.25         0.53         8.35        23.51 
TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50V TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-4110 
       36.00        26.43        19.33        17.85        30.28        14.50 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-3902 
       86.63        11.84        36.03        32.02         6.05        32.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       46.03        13.94         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-DC-6683 TCGA-DY-A1DD TCGA-EI-6881 
       64.01         1.94        38.96         5.03        57.24        16.41 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       31.30        28.57        12.46        26.43 

$`20P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       63.98         6.97         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        26.01        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       10.06        12.03        45.40        12.26        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 
       34.42        41.42        16.24        33.67        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18        28.21        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        61.91        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       13.55        19.10        34.49        37.74        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3580 
       15.39        20.02        10.39        65.98        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45         9.96        49.51         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 
       47.08 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.53               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            109.28             148.01 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             26.22              19.96 
[1] "0.5 - 109.3 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    42  24
  20P LOSS WILD-TYPE 404 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     42   24
  20P LOSS WILD-TYPE  404  138
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON                42                404
  RECTUM               24                138
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P LOSS MUTATED         8        0        7        18         0         1
  20P LOSS WILD-TYPE      96        1       29       155        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          2         14          5        6
  20P LOSS WILD-TYPE        23         16         69         49       57
                    vv
clus                 STAGE IVA STAGE IVB
  20P LOSS MUTATED           3         0
  20P LOSS WILD-TYPE        23         2
D77V4, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   8                 96
  STAGE IA                  0                  1
  STAGE II                  7                 29
  STAGE IIA                18                155
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                2                 16
  STAGE IIIB               14                 69
  STAGE IIIC                5                 49
  STAGE IV                  6                 57
  STAGE IVA                 3                 23
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     1  10  48   8
  20P LOSS WILD-TYPE  19  96 369  59
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                 19
  T2               10                 96
  T3               48                369
  T4                8                 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
  20P LOSS MUTATED    35  21  11
  20P LOSS WILD-TYPE 310 129 104
D77V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               35                310
  N1               21                129
  N2               11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    50   8
  20P LOSS WILD-TYPE 400  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     50    8
  20P LOSS WILD-TYPE  400   80
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               50                400
  1                8                 80
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    33  34
  20P LOSS WILD-TYPE 254 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     33   34
  20P LOSS WILD-TYPE  254  291
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               33                254
  MALE                 34                291
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    48   4
  20P LOSS WILD-TYPE 398  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     48    4
  20P LOSS WILD-TYPE  398   24
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                48                398
  YES                4                 24
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                     38                             4
  20P LOSS WILD-TYPE                  344                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                      21                              3
  20P LOSS WILD-TYPE                   125                             10
D77V10, multiclass
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         38                344
  COLON MUCINOUS ADENOCARCINOMA                 4                 56
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    51   1   5   2
  20P LOSS WILD-TYPE 391   4  32  27
D77V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               51                391
  R1                1                  4
  R2                5                 32
  RX                2                 27
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     0
  20P LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           7    29
  20P LOSS WILD-TYPE                        57   263
D77V13, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       7                 57
  WHITE                                          29                263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  35
  20P LOSS WILD-TYPE   4 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   35
  20P LOSS WILD-TYPE    4  313
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               35                313
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 468 119
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                587 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                119 
$`20Q LOSS MUTATED`
TCGA-AA-3681 TCGA-AA-3952 TCGA-CM-6168 TCGA-D5-6534 TCGA-DM-A1D4 TCGA-NH-A50V 
        5.98         2.01        12.99        43.27        92.75        19.33 

$`20Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       20.19        20.42        17.75        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        79.69        18.18        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.75             148.01 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.16              19.99 
[1] "2.0 - 92.8 (16.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 440 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  440  162
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON                 6                440
  RECTUM                0                162
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q LOSS MUTATED         0        0        0         3         0         0
  20Q LOSS WILD-TYPE     104        1       36       170        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          1          1        0
  20Q LOSS WILD-TYPE        25         18         82         53       63
                    vv
clus                 STAGE IVA STAGE IVB
  20Q LOSS MUTATED           0         0
  20Q LOSS WILD-TYPE        26         2
D78V4, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                104
  STAGE IA                  0                  1
  STAGE II                  0                 36
  STAGE IIA                 3                170
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                0                 18
  STAGE IIIB                1                 82
  STAGE IIIC                1                 53
  STAGE IV                  0                 63
  STAGE IVA                 0                 26
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     0   0   6   0
  20Q LOSS WILD-TYPE  20 106 411  67
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                 20
  T2                0                106
  T3                6                411
  T4                0                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20Q LOSS MUTATED     3   1   2
  20Q LOSS WILD-TYPE 342 149 113
D78V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                3                342
  N1                1                149
  N2                2                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 444  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  444   88
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                444
  1                0                 88
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   3
  20Q LOSS WILD-TYPE 284 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    3
  20Q LOSS WILD-TYPE  284  322
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                284
  MALE                  3                322
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   0
  20Q LOSS WILD-TYPE 442  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE  442   28
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                442
  YES                0                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                      5                             1
  20Q LOSS WILD-TYPE                  377                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                       0                              0
  20Q LOSS WILD-TYPE                   146                             13
D78V10, multiclass
                                clus
vv                               20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          5                377
  COLON MUCINOUS ADENOCARCINOMA                 1                 59
  RECTAL ADENOCARCINOMA                         0                146
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   0   0   0
  20Q LOSS WILD-TYPE 437   5  37  29
D78V11, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                437
  R1                0                  5
  R2                0                 37
  RX                0                 29
[1] 4 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, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           2     2
  20Q LOSS WILD-TYPE                        62   290
D78V13, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       2                 62
  WHITE                                           2                290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE   5 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE    5  344
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                4                344
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   145  37
  21Q LOSS WILD-TYPE 327  84
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               182                411 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                37                 84 
$`21Q LOSS MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4105 
        1.61        39.45        43.76        43.76        37.05        14.53 
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       30.44        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3544 
       38.99         9.07        19.07        34.03        26.01        14.01 
TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 
       19.99        78.08        37.05        19.00        36.00        10.06 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 
       38.99        37.02        14.93        10.06         0.99        17.03 
TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       24.03        18.05        24.00        20.98         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z 
        7.96        13.94        38.04        27.02        42.02        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F 
       15.02        10.98        32.02        31.00        51.98        39.98 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         0.79        22.42         0.20        16.44        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
       16.31        17.85         5.13        65.00        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 
        5.23         3.19        12.69         2.14         3.29        12.20 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       49.08         9.99        20.02         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       22.03        22.98        32.02         5.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 
       29.03        15.02        11.08        11.01        45.40        17.75 
TCGA-D5-6533 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
        1.32         4.80        49.91       140.38         7.50       131.51 
TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       26.47         8.61        31.96        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6314 
       16.24        33.67         0.53        47.41         8.35        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       61.91        36.00        26.43        91.79        46.75        18.18 
TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        9.93        17.85        42.77        24.13        39.48        17.23 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       14.50        15.39        20.02        10.39        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       12.00         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       34.03        12.03         6.05        19.99        20.98        29.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       19.04        19.99        17.03         1.02        48.03        19.99 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03        17.03        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6624 
       10.98        38.96        61.97        41.00         0.69         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.39        21.01        13.97        10.98         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        57.24       129.27        51.48        32.61        20.55 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       20.91        15.85        17.69        16.34        16.41        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
        8.45        31.30         0.39         0.66         0.53         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`21Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       13.94        16.57        37.25        37.02        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.09        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.08        25.18        24.16        24.69        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       16.24        24.92        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07         0.00        29.00        29.00        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       31.07        31.07        53.00        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G 
        0.99        17.03        14.99        34.98         1.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        26.01        37.02        39.06         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       27.42        10.88         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
      109.28        75.95        58.39         1.41         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
      100.01        11.74         1.61         3.06         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 
      124.27        23.05        37.02        25.02        26.04        29.06 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       30.08        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
      130.65        92.75        13.32        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       35.97        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 
       35.74        35.74         6.18        34.42        13.25        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      133.18        28.21        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       39.42        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       74.79        79.69        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       21.90        30.28        11.90        70.03        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-A56L 
       19.10        34.49        37.74        10.39        16.83        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 
       36.03        32.02         8.02        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
        2.01        50.04         0.99        15.95        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       32.02        28.04        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07         1.02        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
        1.94        38.04        38.56         1.45         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        11.01        15.02         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC 
       15.02        27.95        19.99         5.95         5.29        41.36 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       24.13         0.49         2.40        19.96        17.00        18.28 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 
        9.96        49.51        28.57        32.19         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
       12.46        55.76        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.2                0.0 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            140.38             148.01 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             19.99              19.99 
[1] "0.2 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   124  67
  21Q LOSS WILD-TYPE 322  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    124   67
  21Q LOSS WILD-TYPE  322   95
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON               124                322
  RECTUM               67                 95
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q LOSS MUTATED        27        0       11        51         1         1
  21Q LOSS WILD-TYPE      77        1       25       122         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           7          9         27         22       25
  21Q LOSS WILD-TYPE        19          9         56         32       38
                    vv
clus                 STAGE IVA STAGE IVB
  21Q LOSS MUTATED           7         0
  21Q LOSS WILD-TYPE        19         2
D79V4, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  27                 77
  STAGE IA                  0                  1
  STAGE II                 11                 25
  STAGE IIA                51                122
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 7                 19
  STAGE IIIA                9                  9
  STAGE IIIB               27                 56
  STAGE IIIC               22                 32
  STAGE IV                 25                 38
  STAGE IVA                 7                 19
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED     6  34 134  18
  21Q LOSS WILD-TYPE  14  72 283  49
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                6                 14
  T2               34                 72
  T3              134                283
  T4               18                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q LOSS MUTATED    94  51  47
  21Q LOSS WILD-TYPE 251  99  68
D79V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               94                251
  N1               51                 99
  N2               47                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   138  29
  21Q LOSS WILD-TYPE 312  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    138   29
  21Q LOSS WILD-TYPE  312   59
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              138                312
  1               29                 59
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    92 100
  21Q LOSS WILD-TYPE 195 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     92  100
  21Q LOSS WILD-TYPE  195  225
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               92                195
  MALE                100                225
[1] 2 2
[1] FALSE
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   135  12
  21Q LOSS WILD-TYPE 311  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    135   12
  21Q LOSS WILD-TYPE  311   16
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               135                311
  YES               12                 16
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                    116                             8
  21Q LOSS WILD-TYPE                  266                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                      62                              3
  21Q LOSS WILD-TYPE                    84                             10
D79V10, multiclass
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        116                266
  COLON MUCINOUS ADENOCARCINOMA                 8                 52
  RECTAL ADENOCARCINOMA                        62                 84
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   139   1  12   6
  21Q LOSS WILD-TYPE 303   4  25  23
D79V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              139                303
  R1                1                  4
  R2               12                 25
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     4
  21Q LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          17    95
  21Q LOSS WILD-TYPE                        47   197
D79V13, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      17                 47
  WHITE                                          95                197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 108
  21Q LOSS WILD-TYPE   1 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  108
  21Q LOSS WILD-TYPE    1  240
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              108                240
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   149  45
  22Q LOSS WILD-TYPE 323  76
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               194                399 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                 76 
$`22Q LOSS MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       35.11        45.60        13.94        16.57        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       14.53        31.63        30.44        29.19        23.61        22.52 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.61        21.76        23.87        61.84        56.25         9.63 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 
        6.97        38.99         9.07        24.03        37.05        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 
       26.01        12.99        33.99        21.01        13.02        19.99 
TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3697 
       13.94         6.05         2.01        50.04        37.05        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       10.06        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       33.07        32.05        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 
       18.05         2.01        12.99         2.01         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F 
       50.99        13.05        26.01         7.96        13.94        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T 
       27.02        42.02        17.03        14.99        15.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 
       26.01        37.02        39.98        41.00        40.96         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
       22.42         0.20        16.44        14.50        16.31        33.01 
TCGA-AY-A69D TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 
       17.85         1.41         5.65         5.13        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 
        5.23         3.19         1.61         3.06        12.20        14.30 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 
       49.08         1.91        25.02         8.02        29.06        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
        5.03        15.02        15.02        11.08        11.01        45.40 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 
       12.49         1.48         4.80        11.38        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 
      131.51         6.12        26.47        31.96         1.55        16.24 
TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       13.25         8.35        82.39        63.62        61.91        36.00 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       91.79        46.75        18.18        10.98        19.33         9.93 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 
       42.77        29.46        21.90        13.55        14.50        15.39 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       10.39        65.98        12.00        32.02         7.07        20.05 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 
       34.03        34.03        13.94        20.98        29.98        37.02 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 
       19.99         1.02        17.95         1.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 
       14.04         3.98        25.97        12.00        10.98         1.94 
TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 
       38.96        38.56         0.72        10.19         6.05         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       12.39        21.01         5.03        13.97        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 
        4.01         5.03        41.36        51.48         2.40        20.55 
TCGA-EI-6512 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 
       17.69        16.41        28.57         0.39         0.66         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`22Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       15.62        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       42.90        24.33        37.05        37.25        37.02        32.45 
TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       32.91        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
        1.02        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       34.03        29.00         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 
        0.00        36.03         0.99        31.07        53.00        29.98 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       34.03        16.08        34.06        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 
       18.05        38.04         4.01         0.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A024 
       38.07         1.02        35.01         1.02        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72        27.42        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09         0.95        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 
       18.84       109.28        75.95        58.39        32.94       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
      100.01        11.74        12.69         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       13.02        22.03        22.98        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 
       19.59        55.92        20.42        17.75        18.25         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       49.91        13.32         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       35.74         6.18        47.87        34.42        41.42        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        47.41        35.31       133.18        28.21        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       85.48        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV 
       13.78        35.80        26.17        74.79        79.69        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        17.85        16.80        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30        30.28        11.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        19.10        34.49        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 
       16.83        20.02        86.63        11.84        36.03         8.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.04        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       48.03        32.02        28.04         1.02        17.03        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
       51.98        49.97        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.69        26.43         1.81        33.17         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       78.12         7.17        11.01        15.02         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       27.95         5.95         5.29       126.44        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       24.13        32.61         0.49        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       49.51        31.30        32.19         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
       12.46        55.76        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.2                0.0 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.38             148.01 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            18.115             20.910 
[1] "0.2 - 140.4 (18.1)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.5"
D80V2, continuous
D80V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   144  55
  22Q LOSS WILD-TYPE 302 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    144   55
  22Q LOSS WILD-TYPE  302  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON               144                302
  RECTUM               55                107
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q LOSS MUTATED        24        0        9        47         1         1
  22Q LOSS WILD-TYPE      80        1       27       126         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           9         11         29         22       31
  22Q LOSS WILD-TYPE        17          7         54         32       32
                    vv
clus                 STAGE IVA STAGE IVB
  22Q LOSS MUTATED          11         0
  22Q LOSS WILD-TYPE        15         2
D80V4, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  24                 80
  STAGE IA                  0                  1
  STAGE II                  9                 27
  STAGE IIA                47                126
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 9                 17
  STAGE IIIA               11                  7
  STAGE IIIB               29                 54
  STAGE IIIC               22                 32
  STAGE IV                 31                 32
  STAGE IVA                11                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED     4  31 139  27
  22Q LOSS WILD-TYPE  16  75 278  40
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                 16
  T2               31                 75
  T3              139                278
  T4               27                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  22Q LOSS MUTATED    87  67  46
  22Q LOSS WILD-TYPE 258  83  69
D80V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               87                258
  N1               67                 83
  N2               46                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   134  41
  22Q LOSS WILD-TYPE 316  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    134   41
  22Q LOSS WILD-TYPE  316   47
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              134                316
  1               41                 47
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    92 109
  22Q LOSS WILD-TYPE 195 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     92  109
  22Q LOSS WILD-TYPE  195  216
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               92                195
  MALE                109                216
[1] 2 2
[1] FALSE
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   152  10
  22Q LOSS WILD-TYPE 294  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    152   10
  22Q LOSS WILD-TYPE  294   18
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               152                294
  YES               10                 18
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                    134                            10
  22Q LOSS WILD-TYPE                  248                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                      51                              4
  22Q LOSS WILD-TYPE                    95                              9
D80V10, multiclass
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        134                248
  COLON MUCINOUS ADENOCARCINOMA                10                 50
  RECTAL ADENOCARCINOMA                        51                 95
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   137   2  15  11
  22Q LOSS WILD-TYPE 305   3  22  18
D80V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              137                305
  R1                2                  3
  R2               15                 22
  RX               11                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     3
  22Q LOSS WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          24    91
  22Q LOSS WILD-TYPE                        40   201
D80V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      24                 40
  WHITE                                          91                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"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 109
  22Q LOSS WILD-TYPE   2 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  109
  22Q LOSS WILD-TYPE    2  239
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              109                239
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    61  25
  XP LOSS WILD-TYPE 411  96
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               86               507 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               25                96 
$`XP LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3517 
        4.80        42.28        37.02        61.84        56.25        38.99 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3548 TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3697 
        9.07        37.05        33.99        19.99        15.02        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3860 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3968 
       10.06        38.99        31.07        24.00         2.01        21.99 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00R TCGA-AA-A01F 
       24.00         7.96        13.94        19.00         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02F TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-A69D 
       31.00        33.04        39.98         0.20        14.50        17.85 
TCGA-AZ-4614 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CK-5912 
        5.65       100.01        11.74         3.19         3.29        49.08 
TCGA-CM-5348 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-6923 
       22.98        15.02        11.01        13.05        45.40        12.43 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       12.00        24.43        49.91       140.38       131.51         6.12 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6315 
       26.47        31.96        33.67         8.35        65.85        61.91 
TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-T9-A92H 
       26.04        10.98         9.93        15.65        16.80        11.90 
TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 
       70.03        19.10        11.84        12.00        32.02        24.00 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 
       34.03        34.03         2.01         6.05        32.98        19.04 
TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 
        3.98        13.94        23.01        64.01        41.00        38.56 
TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE 
       10.19        13.97        19.99         5.29        57.24       129.27 
TCGA-EI-7002 TCGA-F5-6571 
       11.97        31.30 

$`XP LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        24.33        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       12.99        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        27.02        19.07        27.02        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        10.88        16.44         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        1.61        12.69         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        4.80         1.51        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       35.31       133.18        28.21        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 
       39.42        35.93        36.00        26.43        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
       18.18        19.33        19.33        12.79        17.85        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        39.48        17.23        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       10.39        86.63        65.98        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3598 
       36.03        20.05         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       46.03        20.98         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
        8.98        15.02        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.03       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
              0.2               0.0 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           140.38            148.01 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           22.485            19.990 
[1] "0.2 - 140.4 (22.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D81V2, continuous
D81V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    63  26
  XP LOSS WILD-TYPE 383 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     63   26
  XP LOSS WILD-TYPE  383  136
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON               63               383
  RECTUM              26               136
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP LOSS MUTATED        12        0        5        25         0         0
  XP LOSS WILD-TYPE      92        1       31       148        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           5          1         11         11       14
  XP LOSS WILD-TYPE        21         17         72         43       49
                   vv
clus                STAGE IVA STAGE IVB
  XP LOSS MUTATED           3         1
  XP LOSS WILD-TYPE        23         1
D81V4, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 12                92
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               25               148
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                5                21
  STAGE IIIA               1                17
  STAGE IIIB              11                72
  STAGE IIIC              11                43
  STAGE IV                14                49
  STAGE IVA                3                23
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED     1  12  66  11
  XP LOSS WILD-TYPE  19  94 351  56
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                19
  T2              12                94
  T3              66               351
  T4              11                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
  XP LOSS MUTATED    43  21  26
  XP LOSS WILD-TYPE 302 129  89
D81V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              43               302
  N1              21               129
  N2              26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    62  19
  XP LOSS WILD-TYPE 388  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     62   19
  XP LOSS WILD-TYPE  388   69
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              62               388
  1              19                69
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    39  51
  XP LOSS WILD-TYPE 248 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   51
  XP LOSS WILD-TYPE  248  274
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              39               248
  MALE                51               274
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    67   5
  XP LOSS WILD-TYPE 379  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     67    5
  XP LOSS WILD-TYPE  379   23
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               67               379
  YES               5                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP LOSS MUTATED                     57                             6
  XP LOSS WILD-TYPE                  325                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XP LOSS MUTATED                      21                              4
  XP LOSS WILD-TYPE                   125                              9
D81V10, multiclass
                                clus
vv                               XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        57               325
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    63   0   6   4
  XP LOSS WILD-TYPE 379   5  31  25
D81V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              63               379
  R1               0                 5
  R2               6                31
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     2
  XP LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          12    36
  XP LOSS WILD-TYPE                        52   256
D81V13, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     12                52
  WHITE                                         36               256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  47
  XP LOSS WILD-TYPE   5 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   47
  XP LOSS WILD-TYPE    5  301
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              47               301
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    56  19
  XQ LOSS WILD-TYPE 416 102
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               75               518 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19               102 
$`XQ LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-A567 TCGA-AA-3517 TCGA-AA-3519 
        4.80        42.28        35.11        61.84        38.99         9.07 
TCGA-AA-3522 TCGA-AA-3548 TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3837 TCGA-AA-3860 
       37.05        33.99        19.99        15.02        38.99        31.07 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3989 
       24.00         2.01         2.01        21.99        24.00         7.96 
TCGA-AA-A00D TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02F TCGA-AD-6965 
       19.00         0.99        32.02        31.00        39.98         0.20 
TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 
       14.50        33.01        17.85        11.74         3.19         3.29 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5537 TCGA-D5-6931 
       49.08         1.91        15.02        11.01        45.40        12.00 
TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6808 
       24.43        49.91       140.38       131.51        26.47        33.67 
TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA 
        8.35        65.85        61.91        26.04        10.98         9.93 
TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       16.80        11.90        19.10        11.84        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-4021 
       24.00        34.03         2.01         6.05        32.98         3.98 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 
       13.94        23.01        31.00        64.01        41.00        38.56 
TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE 
       10.19        13.97        19.99         5.29        57.24       129.27 
TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6571 
       32.61        11.97        31.30 

$`XQ LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        24.33        44.91 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        6.97         1.02        13.02         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       24.00        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       34.06        26.01        25.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98         1.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
        6.77        12.10       100.01        29.56         5.23         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         2.14         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
       38.20       130.65        92.75        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        79.69        18.18        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        17.85        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30        21.90        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       86.63        65.98        36.03         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       20.05         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       17.03        46.03        20.98         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
        8.98        15.02        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.03       126.44        41.36        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.2               0.0 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           140.38            148.01 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            23.01             19.99 
[1] "0.2 - 140.4 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D82V2, continuous
D82V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    51  26
  XQ LOSS WILD-TYPE 395 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     51   26
  XQ LOSS WILD-TYPE  395  136
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON               51               395
  RECTUM              26               136
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ LOSS MUTATED        11        0        5        21         0         0
  XQ LOSS WILD-TYPE      93        1       31       152        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           1          2          8         10       15
  XQ LOSS WILD-TYPE        25         16         75         44       48
                   vv
clus                STAGE IVA STAGE IVB
  XQ LOSS MUTATED           3         0
  XQ LOSS WILD-TYPE        23         2
D82V4, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               21               152
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               2                16
  STAGE IIIB               8                75
  STAGE IIIC              10                44
  STAGE IV                15                48
  STAGE IVA                3                23
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED     1  13  54  10
  XQ LOSS WILD-TYPE  19  93 363  57
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                19
  T2              13                93
  T3              54               363
  T4              10                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XQ LOSS MUTATED    38  19  21
  XQ LOSS WILD-TYPE 307 131  94
D82V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              38               307
  N1              19               131
  N2              21                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    52  19
  XQ LOSS WILD-TYPE 398  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     52   19
  XQ LOSS WILD-TYPE  398   69
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              52               398
  1              19                69
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    35  43
  XQ LOSS WILD-TYPE 252 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     35   43
  XQ LOSS WILD-TYPE  252  282
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              35               252
  MALE                43               282
[1] 2 2
[1] FALSE
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    56   4
  XQ LOSS WILD-TYPE 390  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     56    4
  XQ LOSS WILD-TYPE  390   24
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               56               390
  YES               4                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                     45                             6
  XQ LOSS WILD-TYPE                  337                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                      22                              4
  XQ LOSS WILD-TYPE                   124                              9
D82V10, multiclass
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        45               337
  COLON MUCINOUS ADENOCARCINOMA                6                54
  RECTAL ADENOCARCINOMA                       22               124
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    51   0   7   4
  XQ LOSS WILD-TYPE 391   5  30  25
D82V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              51               391
  R1               0                 5
  R2               7                30
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          10    31
  XQ LOSS WILD-TYPE                        54   261
D82V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     10                54
  WHITE                                         31               261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  40
  XQ LOSS WILD-TYPE   5 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   40
  XQ LOSS WILD-TYPE    5  308
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              40               308
[1] 2 2
[1] FALSE
