[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/15076882/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/15089878/transformed.cor.cli.txt"

nPatients in clinical file=624, in cluster file=615, common to both=608
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 608
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               559 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               559 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               492 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               492 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               488 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               488 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              118               490 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              118               490 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               536 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               536 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               97               511 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               97               511 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               588 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               588 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               587 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               587 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               505 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               505 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               544 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               544 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              124               484 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              124               484 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               497 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               497 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              347               261 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              347               261 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              309               299 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              309               299 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              168               440 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              168               440 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              311               297 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              311               297 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              121               487 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              121               487 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               507 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               507 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                47                561 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                47                561 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                27                581 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                27                581 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                84                524 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                84                524 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                76                532 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                76                532 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                481 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                481 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                497 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                497 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               365                243 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               365                243 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                565 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                565 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                593 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                593 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               146                462 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               146                462 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               144                464 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               144                464 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                570 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                570 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               108                500 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               108                500 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                575 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                575 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                589 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                589 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               104                504 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               104                504 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               113                495 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               113                495 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               349                259 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               349                259 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               459                149 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               459                149 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                574 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                574 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                585 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                585 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               98               510 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               98               510 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              107               501 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              107               501 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              135               473 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              135               473 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               76               532 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               76               532 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               591 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               591 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               594 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               594 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               541 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               541 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               565 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               565 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              192               416 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              192               416 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              185               423 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              185               423 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               84               524 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               84               524 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              119               489 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              119               489 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               563 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               563 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               540 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               540 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               604 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               604 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              215               393 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              215               393 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               572 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               572 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74               534 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74               534 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               75               533 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               75               533 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                508 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                508 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                498 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                498 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                534 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                534 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                516 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                516 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                538 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                538 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                70                538 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                70                538 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                588 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                588 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               202                406 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               202                406 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               225                383 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               225                383 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                568 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                568 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                566 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                566 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               335                273 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               335                273 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                96                512 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                96                512 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               374                234 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               374                234 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               404                204 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               404                204 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                545 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                545 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                553 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                553 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                67                541 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                67                541 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                602 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                602 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               190                418 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               190                418 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               199                409 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               199                409 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               89               519 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               89               519 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               531 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               531 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 608 columns.

[1] "Batch" "21"   
[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=99,	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=345,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'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 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "347"                 
freq.contrast "347"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=38,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 608 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "PRIMARY_SITE_OF_DISEASE"               
 [3] "NEOPLASM_DISEASESTAGE"                 
 [4] "PATHOLOGY_T_STAGE"                     
 [5] "PATHOLOGY_N_STAGE"                     
 [6] "PATHOLOGY_M_STAGE"                     
 [7] "GENDER"                                
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "COMPLETENESS_OF_RESECTION"             
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_DISEASESTAGE, 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 
 20 107 413  66 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 107 413  66 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 107 413  66 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 107 413  66 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
342 149 114 
[1] "table(vv)"
vv
 N0  N1  N2 
342 149 114 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
342 149 114 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
342 149 114 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    35  12
  1P GAIN WILD-TYPE 433 103
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               47               536 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               103 
$`1P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-6654 TCGA-AA-3552 
       43.76        44.91        45.60        16.57        23.87        13.02 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3855 TCGA-AA-3973 
       54.02         2.01        15.02        19.00        32.05        13.05 
TCGA-AA-A01D TCGA-AA-A02E TCGA-AD-6888 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 
       10.98         2.96         4.21         0.20        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         0.26        49.08         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       14.04        14.99        15.12         7.53        10.13        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-A026 TCGA-DC-6156 
       13.55        14.50        32.02        46.03         1.94        15.02 
TCGA-DY-A1DF TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 TCGA-G5-6641 
       24.13        10.78         8.45         9.96        26.43 

$`1P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
       42.90        24.33        42.28        35.11        13.94        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-A6-6780 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-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-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-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        47.01        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-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-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        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-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       50.99        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        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        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-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-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-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-A71X 
        0.95        15.75        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-4614 
       18.84        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        62.79        61.41        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-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         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         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        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        35.41        19.43       107.67 
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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        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-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80        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        13.05        12.00        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         9.70        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        12.72        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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        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         0.99 
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-A02G 
       70.03        64.01        10.98        51.98        49.97        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         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
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-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        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         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.2               0.0 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           119.70            140.38 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            15.02             19.51 
[1] "0.2 - 119.7 (15.0)" "0.0 - 140.4 (19.5)"
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    36  11
  1P GAIN WILD-TYPE 406 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     36   11
  1P GAIN WILD-TYPE  406  151
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON               36               406
  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        12         1         0
  1P GAIN WILD-TYPE      97        1       34       159         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         18         75         47       55
                   vv
clus                STAGE IVA STAGE IVB
  1P GAIN MUTATED           6         0
  1P GAIN WILD-TYPE        21         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               12               159
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               3                18
  STAGE IIIB               4                75
  STAGE IIIC               7                47
  STAGE IV                 6                55
  STAGE IVA                6                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
  1P GAIN MUTATED     2   7  32   8
  1P GAIN WILD-TYPE  18 100 381  58
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               2                18
  T2               7               100
  T3              32               381
  T4               8                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
  1P GAIN MUTATED    24  11  13
  1P GAIN WILD-TYPE 318 138 101
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              24               318
  N1              11               138
  N2              13               101
[1] 3 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    30  10
  1P GAIN WILD-TYPE 418  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     30   10
  1P GAIN WILD-TYPE  418   76
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              30               418
  1              10                76
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    20  29
  1P GAIN WILD-TYPE 266 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20   29
  1P GAIN WILD-TYPE  266  293
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              20               266
  MALE                29               293
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                     34                             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
D1V9, multiclass
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        34               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"
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  48
  1P GAIN WILD-TYPE   8 551
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   48
  1P GAIN WILD-TYPE    8  551
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1                 8
  YES              48               551
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    35   1   4   4
  1P GAIN WILD-TYPE 404   4  32  25
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              35               404
  R1               1                 4
  R2               4                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"
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                           5    28
  1P GAIN WILD-TYPE                        55   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                      5                55
  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"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    85  26
  1Q GAIN WILD-TYPE 383  89
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              111               472 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26                89 
$`1Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       43.76        43.76        44.91        35.11        45.60        16.57 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3488 
       36.53        32.45        24.16        24.69        23.87         5.03 
TCGA-AA-3552 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 
       13.02        13.94        78.08        54.02         2.01        47.05 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3858 
       15.02        19.00         5.03        10.06        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3973 TCGA-AA-3994 
       17.03        27.02        12.99        33.01        13.05        27.02 
TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y TCGA-AD-6888 
       10.98        35.01        26.01         2.96        39.98         4.21 
TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
       14.50         0.20        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         0.26        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        14.04        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         7.53        10.13        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        13.38        11.11        35.41        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-3593 TCGA-AG-3600 TCGA-AG-3999 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W 
       34.03         6.05        28.04        36.03        31.00        70.03 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       51.98         1.94        38.04         0.49         0.69         0.72 
TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF 
        9.37        11.01        13.97        15.02       129.27        24.13 
TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7004 TCGA-F5-6464 
       20.55         8.61        10.78        13.64         8.45         9.96 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6641 
        0.69         0.76        26.43 

$`1Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       24.33        42.28        13.94        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        14.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3553 
       12.99         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       61.02         6.05         6.97        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       47.01        11.01         5.98        37.05        36.00        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-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 
        0.00        36.03         0.99        31.07        53.00        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05        31.00         2.01        24.00        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-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        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        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        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-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       27.42        10.88         0.20        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        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        75.25        50.37        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        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         2.24         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         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        20.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       16.01        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       11.51        20.19        20.42        17.75        18.25        43.27 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       11.38        10.26        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-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6569 
      119.93        60.79       117.07        98.24        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        8.35        23.51        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       51.75        45.11        35.93        36.72        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-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80        10.98        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        13.05        12.00        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         9.70        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        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
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-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        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-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95         9.07         1.02        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        49.97        38.96        61.97        41.00         1.45 
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         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        4.73        13.97        78.12         7.17        10.98        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        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-6883 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 
       16.41        11.51        17.46        11.97        37.51        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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.28        55.76        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.2               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            140.38 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            17.85             19.33 
[1] "0.2 - 129.3 (17.9)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    80  34
  1Q GAIN WILD-TYPE 362 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     80   34
  1Q GAIN WILD-TYPE  362  128
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON               80               362
  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        26         2         0
  1Q GAIN WILD-TYPE      90        1       29       145         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         17         64         39       42
                   vv
clus                STAGE IVA STAGE IVB
  1Q GAIN MUTATED           8         0
  1Q GAIN WILD-TYPE        19         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               26               145
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                4                22
  STAGE IIIA               4                17
  STAGE IIIB              15                64
  STAGE IIIC              15                39
  STAGE IV                19                42
  STAGE IVA                8                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
  1Q GAIN MUTATED     4  15  76  21
  1Q GAIN WILD-TYPE  16  92 337  45
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               4                16
  T2              15                92
  T3              76               337
  T4              21                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    54  29  31
  1Q GAIN WILD-TYPE 288 120  83
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              54               288
  N1              29               120
  N2              31                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"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    77  25
  1Q GAIN WILD-TYPE 371  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     77   25
  1Q GAIN WILD-TYPE  371   61
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              77               371
  1              25                61
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    50  66
  1Q GAIN WILD-TYPE 236 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     50   66
  1Q GAIN WILD-TYPE  236  256
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              50               236
  MALE                66               256
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                     74                             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
D2V9, multiclass
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        74               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"
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 113
  1Q GAIN WILD-TYPE   6 486
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  113
  1Q GAIN WILD-TYPE    6  486
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                3                 6
  YES             113               486
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    81   1  10   5
  1Q GAIN WILD-TYPE 358   4  26  24
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              81               358
  R1               1                 4
  R2              10                26
  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                          10    64
  1Q GAIN WILD-TYPE                        50   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                     10                50
  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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    90  24
  2P GAIN WILD-TYPE 378  91
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              114               469 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               24                91 
$`2P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       11.47        43.76        37.02        34.65        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       30.44        32.71        29.16        24.16        24.69        23.87 
TCGA-AA-3496 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3562 
        1.02         9.07        34.03        29.00        29.00        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 
       50.04        15.02        37.05        10.06        35.05        33.07 
TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-A00L TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X 
       24.03        16.08        38.04        31.00         1.02        26.01 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
       21.37         4.21         5.79        22.42        27.42        16.44 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 
       16.31         0.20        18.84         5.13         3.19         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 
        0.26         0.10        40.34        21.99         8.02        29.06 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        17.03        15.02        14.04        29.03        21.99 
TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
       45.40        11.51         4.80        17.13        14.30        13.41 
TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 TCGA-G4-6299 
        7.50         7.76        35.97         8.61         8.35        74.56 
TCGA-G4-6310 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A6GC TCGA-NH-A8F7 
       45.11        47.15        52.80        18.18        12.79        13.05 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       29.46        32.98        30.28        24.13        39.48        17.23 
TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3593 
       16.83        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L 
       19.99        19.99         1.02         1.02         0.99        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-5917 
       31.00        70.03        38.04        26.43        10.19        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        7.17        10.98        12.99        12.00        15.02        36.00 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 
       13.05       129.27        51.48        20.55        16.31        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        9.96        37.51         0.46        18.28        55.76        47.08 

$`2P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.57        37.05        37.25        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02         1.02        37.05        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
        6.97         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-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-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-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-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        19.04         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-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-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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01        33.04        35.01        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-6889 
       41.00        39.98        18.05        40.96         0.07        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-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        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         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.25         3.29         0.33         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        70.16        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       25.02        26.04        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-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-D5-6529 
       10.06        12.03        12.26        19.59        13.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64         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-A288 
       44.32       131.51       135.65       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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        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        35.41        19.43       107.67        28.21 
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-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        51.75        39.42        35.93        36.72        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-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       91.79        46.75        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       15.65        12.00        42.77         8.42        31.30         9.70 
TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       70.03        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       10.39        14.50        15.39        20.02        10.39        11.84 
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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99         0.99         1.02        36.95 
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-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       19.99        28.04        36.03        14.04        17.03        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-A01Y TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         0.72         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 
        6.97         9.37         4.73        13.97        11.01        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       13.97        10.98        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97         8.45        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-G5-6641 
       26.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            140.38 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            20.27             19.04 
[1] "0.1 - 129.3 (20.3)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    79  41
  2P GAIN WILD-TYPE 363 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     79   41
  2P GAIN WILD-TYPE  363  121
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON               79               363
  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        29         0         2
  2P GAIN WILD-TYPE      88        1       28       142        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          3         19         15       11
  2P GAIN WILD-TYPE        20         18         60         39       50
                   vv
clus                STAGE IVA STAGE IVB
  2P GAIN MUTATED           7         1
  2P GAIN WILD-TYPE        20         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               29               142
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                6                20
  STAGE IIIA               3                18
  STAGE IIIB              19                60
  STAGE IIIC              15                39
  STAGE IV                11                50
  STAGE IVA                7                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
  2P GAIN MUTATED     2  19  88  10
  2P GAIN WILD-TYPE  18  88 325  56
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               2                18
  T2              19                88
  T3              88               325
  T4              10                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
  2P GAIN MUTATED    57  29  32
  2P GAIN WILD-TYPE 285 120  82
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              57               285
  N1              29               120
  N2              32                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    80  19
  2P GAIN WILD-TYPE 368  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     80   19
  2P GAIN WILD-TYPE  368   67
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              80               368
  1              19                67
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    61  59
  2P GAIN WILD-TYPE 225 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     61   59
  2P GAIN WILD-TYPE  225  263
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              61               225
  MALE                59               263
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                     73                             6
  2P GAIN WILD-TYPE                  308                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                      41                              0
  2P GAIN WILD-TYPE                   105                             13
D3V9, multiclass
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        73               308
  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"
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3 117
  2P GAIN WILD-TYPE   6 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3  117
  2P GAIN WILD-TYPE    6  482
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                3                 6
  YES             117               482
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    84   3   5  10
  2P GAIN WILD-TYPE 355   2  31  19
D3V11, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              84               355
  R1               3                 2
  R2               5                31
  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                          16    67
  2P GAIN WILD-TYPE                        44   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                     16                44
  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"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    87  25
  2Q GAIN WILD-TYPE 381  90
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              112               471 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               25                90 
$`2Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 
       11.47        43.76        34.65        36.53        14.53        30.44 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3496 
       32.71        29.16        24.16        24.69        23.87         1.02 
TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3562 TCGA-AA-3673 
        9.07        34.03        29.00        29.00        19.99        50.04 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 
       15.02        37.05         5.03        10.06        35.05        33.07 
TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AD-6548 
       24.03        16.08        31.00         1.02        26.01        21.37 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 
        4.21         5.79        22.42        27.42        16.44        16.31 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
       18.84         5.13         3.19         0.26        40.34        21.99 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        8.02        29.06         5.03        15.02        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 
       21.99        14.99        45.40        11.51         4.80        17.13 
TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 
        7.50         7.76        14.04        35.97         8.61         8.35 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       74.56        45.11        39.42        47.15        52.80        18.18 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 
       12.79        13.05        29.46        32.98        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       39.48        17.23        10.39        16.83        15.39        86.63 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 
       65.98        36.03        46.03        34.03        19.99        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N 
        1.02        48.03         1.02         0.99        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-5917 TCGA-CL-5918 
       70.03        38.04        26.43        10.19        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       12.99        12.00        15.02        36.00        13.05       129.27 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
        2.40        20.55        16.31        13.64         9.96        37.51 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.76         0.46        18.28        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       16.57        37.05        37.25        37.02        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-3697 
       47.01        11.01         5.98        19.00        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        19.04         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-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-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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-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-6196 
        0.92        14.50        27.09         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        2.24         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 
        0.33         0.10         1.35        17.56       102.44        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         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        16.01 
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        13.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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 
       51.75        35.93        36.72        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        12.00 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2691 
       42.77         8.42        31.30         9.70        70.03        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 
       13.55        19.10        12.72        37.74        14.50        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-3594 TCGA-AG-3598 
       36.03        20.05        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        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         1.02        32.98         0.99         0.99 
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-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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03         9.07         1.02        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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 
        0.49         1.45         0.69         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        6.05         6.97         9.37         4.73        13.97        10.98 
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        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         0.49        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-G5-6235 TCGA-G5-6641 
        1.12        55.76        26.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.26              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            140.38 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            19.99             19.04 
[1] "0.3 - 129.3 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    75  43
  2Q GAIN WILD-TYPE 367 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     75   43
  2Q GAIN WILD-TYPE  367  119
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON               75               367
  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        27         0         2
  2Q GAIN WILD-TYPE      88        1       28       144        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           7          3         18         16       12
  2Q GAIN WILD-TYPE        19         18         61         38       49
                   vv
clus                STAGE IVA STAGE IVB
  2Q GAIN MUTATED           5         1
  2Q GAIN WILD-TYPE        22         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               27               144
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                7                19
  STAGE IIIA               3                18
  STAGE IIIB              18                61
  STAGE IIIC              16                38
  STAGE IV                12                49
  STAGE IVA                5                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
  2Q GAIN MUTATED     2  19  86  10
  2Q GAIN WILD-TYPE  18  88 327  56
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                18
  T2              19                88
  T3              86               327
  T4              10                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
  2Q GAIN MUTATED    55  28  33
  2Q GAIN WILD-TYPE 287 121  81
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              55               287
  N1              28               121
  N2              33                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    79  18
  2Q GAIN WILD-TYPE 369  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     79   18
  2Q GAIN WILD-TYPE  369   68
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              79               369
  1              18                68
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    61  57
  2Q GAIN WILD-TYPE 225 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     61   57
  2Q GAIN WILD-TYPE  225  265
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              61               225
  MALE                57               265
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                     69                             6
  2Q GAIN WILD-TYPE                  312                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                      43                              0
  2Q GAIN WILD-TYPE                   103                             13
D4V9, multiclass
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        69               312
  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"
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4 114
  2Q GAIN WILD-TYPE   5 485
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4  114
  2Q GAIN WILD-TYPE    5  485
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                4                 5
  YES             114               485
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    83   2   6   8
  2Q GAIN WILD-TYPE 356   3  30  21
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              83               356
  R1               2                 3
  R2               6                30
  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                          18    64
  2Q GAIN WILD-TYPE                        42   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                     18                42
  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"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    53  13
  3P GAIN WILD-TYPE 415 102
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               66               517 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               102 
$`3P GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6782 
       11.47        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         1.94         2.24        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-3593 TCGA-AG-3612 TCGA-AG-3726 
        9.70        20.02        10.39        34.03        19.99         7.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A020 
        1.02        36.03        14.04         9.07        12.00        10.98 
TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DY-A1DC 
        9.37        10.98        12.99        15.02        12.95        41.36 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
      129.27         2.40        18.28        11.97        28.57        32.19 

$`3P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        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-A6-6137 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-A6-6654 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-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-3561 
       24.00        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-3672 
       61.02        78.08         6.05         6.97        54.02         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-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-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-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-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-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-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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        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         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
        0.46         0.92        14.50        27.09        16.31        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         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-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
        5.03        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        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-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-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       26.04        35.80        26.17        91.79        47.15        52.80 
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-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        30.28        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        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       14.50        16.83        15.39        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-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 
       12.03         6.05         0.99        15.95        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         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-4007 TCGA-AG-4008 
       48.03        32.02        19.99        28.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        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         0.49         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         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        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 
       12.00        13.97        36.00        10.98        30.05        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         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 
       37.51        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         0.46        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            140.38 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            15.07             19.33 
[1] "0.2 - 129.3 (15.1)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    44  27
  3P GAIN WILD-TYPE 398 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     44   27
  3P GAIN WILD-TYPE  398  135
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON               44               398
  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       153         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         16         73         48       52
                   vv
clus                STAGE IVA STAGE IVB
  3P GAIN MUTATED           5         2
  3P GAIN WILD-TYPE        22         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               153
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                5                21
  STAGE IIIA               5                16
  STAGE IIIB               6                73
  STAGE IIIC               6                48
  STAGE IV                 9                52
  STAGE IVA                5                22
  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  94 365  58
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                18
  T2              13                94
  T3              48               365
  T4               8                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 GAIN MUTATED    34  20  18
  3P GAIN WILD-TYPE 308 129  96
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              34               308
  N1              20               129
  N2              18                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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    43  14
  3P GAIN WILD-TYPE 405  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     43   14
  3P GAIN WILD-TYPE  405   72
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              43               405
  1              14                72
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    38  34
  3P GAIN WILD-TYPE 248 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   34
  3P GAIN WILD-TYPE  248  288
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              38               248
  MALE                34               288
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                     39                             5
  3P GAIN WILD-TYPE                  342                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                      26                              1
  3P GAIN WILD-TYPE                   120                             12
D5V9, multiclass
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        39               342
  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"
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  71
  3P GAIN WILD-TYPE   8 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   71
  3P GAIN WILD-TYPE    8  528
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                1                 8
  YES              71               528
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    52   0   3   3
  3P GAIN WILD-TYPE 387   5  33  26
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              52               387
  R1               0                 5
  R2               3                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"
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                        53   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                53
  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"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    71  18
  3Q GAIN WILD-TYPE 397  97
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               89               494 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18                97 
$`3Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6137 
       11.47        43.76        37.02        36.53        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3532 TCGA-AA-3552 
       25.08        20.61        21.76        20.28        29.00        13.02 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3685 
       19.99        19.99        78.08         2.01        14.01        37.05 
TCGA-AA-3842 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3979 
       37.02        17.03        24.03        16.08        26.01        24.00 
TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6899 
       34.03         1.02        33.04        41.00         4.21         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4614 
       22.42         0.20        14.50         0.95        17.85         5.65 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6161 
       29.56         1.94         2.24         8.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6539 
       14.04        29.03        13.05        10.06        15.12        12.49 
TCGA-D5-6924 TCGA-DM-A285 TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6294 TCGA-G4-6303 
       14.30         6.12        14.04         1.55        28.21        65.85 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-QL-A97D 
       39.42        35.93        13.78        46.75        12.79         9.70 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3593 TCGA-AG-3612 
       37.74        10.39        20.02        10.39        34.03        19.99 
TCGA-AG-3726 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L 
        7.99         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        10.98        12.99        15.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 
       12.95        13.05        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-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        22.52        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3534 
        8.05        19.07         0.00        19.07        34.03        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-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       24.00        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 
       61.02         6.05         6.97        54.02         0.92        50.04 
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-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-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-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-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        50.99        13.05        34.06        25.02        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 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07        35.01         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37        56.55         0.79         0.72        27.42 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       15.75         0.20        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        75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         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-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        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        13.51        11.51        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-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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-A28A 
       44.32       131.51       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-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        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        35.41        19.43       107.67         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-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        51.75        45.11        36.72        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       22.09        26.04        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        30.28        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       17.23        43.04        13.55        19.10        12.72        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        15.39        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-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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-4022 
       32.02        19.99        28.04         1.02        17.03         0.99 
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-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         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-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         0.49         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-6624 
        1.81        10.19         6.05         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       13.97         7.17        11.01        15.02        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       36.00        10.98        30.05        10.06         5.29       126.44 
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-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 
       17.46         8.45         9.96        37.51        31.30         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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.2               0.0 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.12            140.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            15.12             19.51 
[1] "0.2 - 78.1 (15.1)"  "0.0 - 140.4 (19.5)"
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    62  34
  3Q GAIN WILD-TYPE 380 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     62   34
  3Q GAIN WILD-TYPE  380  128
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON               62               380
  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       147         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           6          6         11          9       12
  3Q GAIN WILD-TYPE        20         15         68         45       49
                   vv
clus                STAGE IVA STAGE IVB
  3Q GAIN MUTATED           7         2
  3Q GAIN WILD-TYPE        20         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               147
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               6                15
  STAGE IIIB              11                68
  STAGE IIIC               9                45
  STAGE IV                12                49
  STAGE IVA                7                20
  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  15  67  10
  3Q GAIN WILD-TYPE  16  92 346  56
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               4                16
  T2              15                92
  T3              67               346
  T4              10                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
  3Q GAIN MUTATED    44  30  22
  3Q GAIN WILD-TYPE 298 119  92
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              44               298
  N1              30               119
  N2              22                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"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    59  19
  3Q GAIN WILD-TYPE 389  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     59   19
  3Q GAIN WILD-TYPE  389   67
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              59               389
  1              19                67
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    50  47
  3Q GAIN WILD-TYPE 236 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     50   47
  3Q GAIN WILD-TYPE  236  275
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              50               236
  MALE                47               275
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                     56                             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
D6V9, multiclass
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        56               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"
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  95
  3Q GAIN WILD-TYPE   7 504
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   95
  3Q GAIN WILD-TYPE    7  504
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                2                 7
  YES              95               504
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    72   0   3   4
  3Q GAIN WILD-TYPE 367   5  33  25
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              72               367
  R1               0                 5
  R2               3                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"
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                           9    52
  3Q GAIN WILD-TYPE                        51   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                      9                51
  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"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    15   4
  4P GAIN WILD-TYPE 453 111
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               564 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               111 
$`4P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-A56B TCGA-AA-3560 TCGA-AA-3982 
       11.47        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         0.99        37.02        11.01        13.05        51.48 
TCGA-EI-6510 
       18.28 

$`4P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       24.33        42.28        44.91        35.11        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-A5ZU 
       19.66        20.28        16.24        24.92        61.84         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-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-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-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-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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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 
        4.21        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-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        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        75.25        50.37 
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        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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 
        1.94         2.24         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         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        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        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        35.41        19.43       107.67 
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        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        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        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30         9.70        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        12.72 
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-3593 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-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        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         1.02        32.98         0.99         0.99 
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-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        10.98        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        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        37.51        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         0.46        18.28        55.76        47.08        26.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            56.25            140.38 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            19.99             19.07 
[1] "1.0 - 56.2 (20.0)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   9
  4P GAIN WILD-TYPE 431 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    9
  4P GAIN WILD-TYPE  431  153
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON               11               431
  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       167        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         21         75         53       60
                   vv
clus                STAGE IVA STAGE IVB
  4P GAIN MUTATED           4         0
  4P GAIN WILD-TYPE        23         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               167
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               0                21
  STAGE IIIB               4                75
  STAGE IIIC               1                53
  STAGE IV                 1                60
  STAGE IVA                4                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
  4P GAIN MUTATED     0   5  15   0
  4P GAIN WILD-TYPE  20 102 398  66
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                20
  T2               5               102
  T3              15               398
  T4               0                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
  4P GAIN MUTATED    10   6   4
  4P GAIN WILD-TYPE 332 143 110
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              10               332
  N1               6               143
  N2               4               110
[1] 3 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 436  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12    4
  4P GAIN WILD-TYPE  436   82
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              12               436
  1               4                82
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  14
  4P GAIN WILD-TYPE 280 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   14
  4P GAIN WILD-TYPE  280  308
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               280
  MALE                14               308
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                     11                             0
  4P GAIN WILD-TYPE                  370                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                       9                              0
  4P GAIN WILD-TYPE                   137                             13
D7V9, multiclass
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        11               370
  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"
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  20
  4P GAIN WILD-TYPE   9 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   20
  4P GAIN WILD-TYPE    9  579
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 9
  YES              20               579
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    17   0   0   0
  4P GAIN WILD-TYPE 422   5  36  29
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              17               422
  R1               0                 5
  R2               0                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"
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                        55   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                55
  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"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    14   6
  4Q GAIN WILD-TYPE 454 109
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               563 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               109 
$`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 
       13.05        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        42.28        44.91        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 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-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-3561 
       24.00        17.95        29.95        23.01        20.98        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-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-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-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-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-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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        5.79        22.42        27.42        10.88         0.20         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        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
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         1.94         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-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        13.51        11.51 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05        12.00 
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         9.70 
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        12.72        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-3593 TCGA-AG-3594 
       20.05        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-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        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         0.99        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         0.49         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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00        10.98        30.05        12.95        10.06         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-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        37.51        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 
        0.46        18.28        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            140.38 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            28.65             19.00 
[1] "3.2 - 56.2 (28.6)"  "0.0 - 140.4 (19.0)"
[1] "hr=" "1.3"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   5
  4Q GAIN WILD-TYPE 426 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    5
  4Q GAIN WILD-TYPE  426  157
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON               16               426
  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       166        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         21         74         52       57
                   vv
clus                STAGE IVA STAGE IVB
  4Q GAIN MUTATED           2         0
  4Q GAIN WILD-TYPE        25         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               166
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                0                26
  STAGE IIIA               0                21
  STAGE IIIB               5                74
  STAGE IIIC               2                52
  STAGE IV                 4                57
  STAGE IVA                2                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
  4Q GAIN MUTATED     0   3  16   2
  4Q GAIN WILD-TYPE  20 104 397  64
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                20
  T2               3               104
  T3              16               397
  T4               2                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
  4Q GAIN MUTATED     8   6   7
  4Q GAIN WILD-TYPE 334 143 107
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8               334
  N1               6               143
  N2               7               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"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    13   6
  4Q GAIN WILD-TYPE 435  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     13    6
  4Q GAIN WILD-TYPE  435   80
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              13               435
  1               6                80
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6  15
  4Q GAIN WILD-TYPE 280 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   15
  4Q GAIN WILD-TYPE  280  307
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               6               280
  MALE                15               307
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                     16                             0
  4Q GAIN WILD-TYPE                  365                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                       5                              0
  4Q GAIN WILD-TYPE                   141                             13
D8V9, multiclass
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        16               365
  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"
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  21
  4Q GAIN WILD-TYPE   9 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   21
  4Q GAIN WILD-TYPE    9  578
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 9
  YES              21               578
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    16   0   2   0
  4Q GAIN WILD-TYPE 423   5  34  29
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              16               423
  R1               0                 5
  R2               2                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"
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                        56   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                56
  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"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    80  19
  5P GAIN WILD-TYPE 388  96
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               99               484 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                96 
$`5P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       11.47        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-6196 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6603 
       16.44         0.92         0.20        18.84        49.41        29.56 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 
        1.94         2.24        25.02        13.02        16.01        15.02 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6924 
       14.99        13.02        11.01        19.59        17.75        14.30 
TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28K 
       13.41        12.00        12.59         7.50         6.12        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6307 
       95.18        13.38         1.55        35.41        82.39        55.04 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-3911 
       46.75        47.15        12.79         8.42        30.28        37.74 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 
       20.02        10.39        86.63        65.98        36.03        46.03 
TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H 
       19.99         1.02        17.03        36.03         1.02        25.97 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       36.03        12.00        31.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-5869 TCGA-DC-6156 
       38.04         0.69         0.72        10.19        12.99        15.02 
TCGA-DC-6683 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 TCGA-F5-6702 
       10.06         2.40        16.31        11.51         9.96        28.57 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       32.19         0.53         0.76 

$`5P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.05        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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        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-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        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-3561 
       21.01        17.95        29.95        23.01        20.98        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-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        36.00         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-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-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-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-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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         4.21        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88         0.20         0.46        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        15.75        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        75.25        50.37        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        61.41         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 
       20.02        37.02        26.04         8.02        27.02        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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        12.99        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.26        13.51        11.51        20.19        20.42        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       12.43         9.04         9.44        11.64         1.51        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-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-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       35.97        60.79       117.07         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        19.43       107.67        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        51.75        45.11        39.42        35.93        36.72 
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-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.17        91.79        52.80        18.18        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        13.05        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       29.46        32.98        31.30         9.70        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        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 
       10.39        14.50        16.83        15.39        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        1.02        32.98         0.99         0.99        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-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        14.04        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
       13.94         6.02        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       61.97         0.49         1.45        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.17        10.98        11.01        15.02        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       36.00        10.98        30.05        12.95        13.05         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-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-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-F5-6465 
       10.78        13.64        17.46        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
       31.30         0.39         0.66         0.69         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.2               0.0 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            98.24            140.38 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            17.03             19.33 
[1] "0.2 - 98.2 (17.0)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    67  36
  5P GAIN WILD-TYPE 375 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     67   36
  5P GAIN WILD-TYPE  375  126
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON               67               375
  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       145         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         16         66         38       48
                   vv
clus                STAGE IVA STAGE IVB
  5P GAIN MUTATED           5         1
  5P GAIN WILD-TYPE        22         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               145
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                3                23
  STAGE IIIA               5                16
  STAGE IIIB              13                66
  STAGE IIIC              16                38
  STAGE IV                13                48
  STAGE IVA                5                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
  5P GAIN MUTATED     1  20  69  13
  5P GAIN WILD-TYPE  19  87 344  53
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                19
  T2              20                87
  T3              69               344
  T4              13                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
  5P GAIN MUTATED    45  31  26
  5P GAIN WILD-TYPE 297 118  88
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               297
  N1              31               118
  N2              26                88
[1] 3 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 378  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     70   18
  5P GAIN WILD-TYPE  378   68
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              70               378
  1              18                68
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    48  55
  5P GAIN WILD-TYPE 238 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     48   55
  5P GAIN WILD-TYPE  238  267
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              48               238
  MALE                55               267
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                     59                             8
  5P GAIN WILD-TYPE                  322                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                      36                              0
  5P GAIN WILD-TYPE                   110                             13
D9V9, multiclass
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        59               322
  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"
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 100
  5P GAIN WILD-TYPE   6 499
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  100
  5P GAIN WILD-TYPE    6  499
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3                 6
  YES             100               499
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    76   1   9   2
  5P GAIN WILD-TYPE 363   4  27  27
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              76               363
  R1               1                 4
  R2               9                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"
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                        46   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                46
  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"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    49  12
  5Q GAIN WILD-TYPE 419 103
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               61               522 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               103 
$`5Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       11.47        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        15.75        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        16.01        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 
       47.15        12.79         8.42        20.02        10.39        65.98 
TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-4007 TCGA-AG-A00H 
       36.03        19.99         1.02        17.03         1.02        25.97 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 
       12.00        31.00        41.00        38.04         0.69         0.72 
TCGA-DC-6683 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6811 
       10.06        16.31        11.51        11.97         9.96        32.19 
TCGA-F5-6814 
        0.53 

$`5Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.02        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-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        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-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 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-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        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-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-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        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21        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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84        75.25        50.37        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        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       61.41         6.77        12.10       100.01         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00        14.04        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-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        13.51        11.51        20.19 
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         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       35.80        26.17        91.79        52.80        18.18        10.98 
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        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       42.77        29.46        32.98        31.30         9.70        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-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        12.72        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        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-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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         0.99        19.99        36.95        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-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        38.96        61.97         0.49         1.45 
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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       36.00        10.98        30.05        12.95        13.05         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-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        8.61        10.78        13.64        17.46         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       31.30        28.57         0.39         0.66         0.69         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.53              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            95.18            140.38 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            16.44             19.38 
[1] "0.5 - 95.2 (16.4)"  "0.0 - 140.4 (19.4)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    40  24
  5Q GAIN WILD-TYPE 402 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     40   24
  5Q GAIN WILD-TYPE  402  138
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON               40               402
  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       155         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         17         73         46       52
                   vv
clus                STAGE IVA STAGE IVB
  5Q GAIN MUTATED           2         1
  5Q GAIN WILD-TYPE        25         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               155
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               4                17
  STAGE IIIB               6                73
  STAGE IIIC               8                46
  STAGE IV                 9                52
  STAGE IVA                2                25
  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  93 371  58
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                20
  T2              14                93
  T3              42               371
  T4               8                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
  5Q GAIN MUTATED    30  20  13
  5Q GAIN WILD-TYPE 312 129 101
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              30               312
  N1              20               129
  N2              13               101
[1] 3 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 404  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     44   11
  5Q GAIN WILD-TYPE  404   75
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              44               404
  1              11                75
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    29  35
  5Q GAIN WILD-TYPE 257 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     29   35
  5Q GAIN WILD-TYPE  257  287
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              29               257
  MALE                35               287
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                     36                             4
  5Q GAIN WILD-TYPE                  345                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                      24                              0
  5Q GAIN WILD-TYPE                   122                             13
D10V9, multiclass
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        36               345
  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"
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  63
  5Q GAIN WILD-TYPE   8 536
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   63
  5Q GAIN WILD-TYPE    8  536
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                 8
  YES              63               536
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    47   0   6   1
  5Q GAIN WILD-TYPE 392   5  30  28
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              47               392
  R1               0                 5
  R2               6                30
  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                        50   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                50
  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"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    96  20
  6P GAIN WILD-TYPE 372  95
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              116               467 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               20                95 
$`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-6196 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 
        0.95         0.20        17.26        22.36        65.00         1.35 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 
       15.62        21.99         8.02        13.02        29.06        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 
       16.01         5.03        15.02        13.02        15.02        19.59 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6929 
       11.51         1.32        17.13        12.49         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       11.38         7.50        14.04       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6310 
        8.61        13.38        13.45         1.55        82.39        45.11 
TCGA-G4-6311 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW 
       39.42        91.79        46.75        10.98        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 
        9.70        30.28        24.13        43.04        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3612 TCGA-AG-3728 
       14.50        15.39        65.98        46.03        19.99        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 
        1.02         1.02        14.04         1.02         0.99        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 
        9.07        12.00        31.00         0.72        10.19         6.05 
TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DE 
        9.37        12.99        12.00        15.02        36.00       129.27 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       20.55        15.85        17.69        37.51        28.57         0.39 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`6P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        42.28        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-A6-5661 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-A6-6137 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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        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-A5ZU 
       19.66        20.28        16.24        24.92        61.84         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-3538 
        8.05        19.07         0.00        19.07        34.03        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-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-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-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        24.00        19.07        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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        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         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        15.75        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        75.25        50.37        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        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        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         1.94         2.24         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         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 
        0.10        17.56       102.44        40.34        70.16        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        25.02        26.04        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.98        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
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-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64         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-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-A285 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 TCGA-F4-6463 
       81.37       119.93        35.97        60.79        11.11        13.64 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        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        35.41        19.43       107.67        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-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        35.93        36.72        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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80        18.18        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        13.05        12.00        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       31.30        70.03        39.48        17.23        13.55        19.10 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       12.72        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-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
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-4008 TCGA-AG-A002 
       32.02        19.99        28.04        36.03        17.03        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-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        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         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69        26.43         1.81         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        13.97        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        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-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        31.30        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         0.46        55.76        47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            140.38 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           18.935            19.070 
[1] "0.2 - 129.3 (18.9)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83  39
  6P GAIN WILD-TYPE 359 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83   39
  6P GAIN WILD-TYPE  359  123
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON               83               359
  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       147         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           6          7         21         15       15
  6P GAIN WILD-TYPE        20         14         58         39       46
                   vv
clus                STAGE IVA STAGE IVB
  6P GAIN MUTATED           9         1
  6P GAIN WILD-TYPE        18         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               147
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III                6                20
  STAGE IIIA               7                14
  STAGE IIIB              21                58
  STAGE IIIC              15                39
  STAGE IV                15                46
  STAGE IVA                9                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
  6P GAIN MUTATED     6  18  86  14
  6P GAIN WILD-TYPE  14  89 327  52
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6                14
  T2              18                89
  T3              86               327
  T4              14                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
  6P GAIN MUTATED    54  31  38
  6P GAIN WILD-TYPE 288 118  76
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              54               288
  N1              31               118
  N2              38                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83  24
  6P GAIN WILD-TYPE 365  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83   24
  6P GAIN WILD-TYPE  365   62
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              83               365
  1              24                62
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    53  71
  6P GAIN WILD-TYPE 233 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     53   71
  6P GAIN WILD-TYPE  233  251
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              53               233
  MALE                71               251
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                     73                            10
  6P GAIN WILD-TYPE                  308                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                      38                              1
  6P GAIN WILD-TYPE                   108                             12
D11V9, multiclass
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        73               308
  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"
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     7 117
  6P GAIN WILD-TYPE   2 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7  117
  6P GAIN WILD-TYPE    2  482
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                7                 2
  YES             117               482
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    91   0  11   4
  6P GAIN WILD-TYPE 348   5  25  25
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              91               348
  R1               0                 5
  R2              11                25
  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                        45   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                45
  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"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    86  17
  6Q GAIN WILD-TYPE 382  98
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              103               480 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17                98 
$`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-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 
        0.95         0.20        17.26         5.65        22.36        65.00 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        1.35        15.62        21.99         8.02        13.02        29.06 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 
       16.01         5.03        15.02        13.02        15.02        19.59 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6929 
       11.51         1.32        17.13        12.49         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       11.38         7.50        14.04       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 
       13.38        13.45        82.39        74.56        45.11        39.42 
TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       91.79        10.98        12.79        29.46         9.70        30.28 
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       24.13        37.74        10.39        14.50        15.39        65.98 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 
       19.99        29.98         1.02         1.02         1.02         0.99 
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        12.99        12.00        15.02        36.00 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 
       51.48        20.55        15.85        17.69        37.51        28.57 
TCGA-F5-6810 
        0.39 

$`6Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        42.28        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-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       19.07        34.03         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-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-3968 TCGA-AA-3971 
       24.00         2.01        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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        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         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        15.75        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        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41        32.94         5.13        83.80        62.79        61.41 
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         1.94         2.24         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         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        22.03        22.98 
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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
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-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64         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-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-A285 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 
       81.37       119.93        35.97        60.79        98.24        11.11 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21         8.35        23.51        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        35.93        36.72 
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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        46.75        47.15        52.80        18.18        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        13.05        12.00        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       32.98         8.42        31.30        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 
       43.04        13.55        19.10        12.72        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-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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
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         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       28.04        36.03        14.04        17.03        20.98        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-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         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69        26.43         1.81         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        30.05        12.95        13.05        10.06 
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-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-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        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-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30        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         0.46        18.28        55.76        47.08        26.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.2               0.0 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           117.07            140.38 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           17.130            19.215 
[1] "0.2 - 117.1 (17.1)" "0.0 - 140.4 (19.2)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    75  34
  6Q GAIN WILD-TYPE 367 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     75   34
  6Q GAIN WILD-TYPE  367  128
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON               75               367
  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       151         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           6          6         18         13       13
  6Q GAIN WILD-TYPE        20         15         61         41       48
                   vv
clus                STAGE IVA STAGE IVB
  6Q GAIN MUTATED          11         1
  6Q GAIN WILD-TYPE        16         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               151
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               6                15
  STAGE IIIB              18                61
  STAGE IIIC              13                41
  STAGE IV                13                48
  STAGE IVA               11                16
  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  90 338  51
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                16
  T2              17                90
  T3              75               338
  T4              15                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
  6Q GAIN MUTATED    48  29  33
  6Q GAIN WILD-TYPE 294 120  81
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              48               294
  N1              29               120
  N2              33                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"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    72  24
  6Q GAIN WILD-TYPE 376  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     72   24
  6Q GAIN WILD-TYPE  376   62
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              72               376
  1              24                62
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    49  62
  6Q GAIN WILD-TYPE 237 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     49   62
  6Q GAIN WILD-TYPE  237  260
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              49               237
  MALE                62               260
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                     67                             8
  6Q GAIN WILD-TYPE                  314                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                      34                              0
  6Q GAIN WILD-TYPE                   112                             13
D12V9, multiclass
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        67               314
  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"
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7 104
  6Q GAIN WILD-TYPE   2 495
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  104
  6Q GAIN WILD-TYPE    2  495
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                 2
  YES             104               495
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    81   0  10   4
  6Q GAIN WILD-TYPE 358   5  26  25
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              81               358
  R1               0                 5
  R2              10                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"
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                        46   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                46
  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"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   264  68
  7P GAIN WILD-TYPE 204  47
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              332               251 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68                47 
$`7P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        45.60        13.94        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.19        29.16        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 
       24.16        20.61        24.69        23.87        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       24.92        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 
       37.05         1.02        35.01        58.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07        36.03         0.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       14.01        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
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-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
        5.03        85.05        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       37.02        14.93         0.00        32.05         0.99        31.07 
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-3941 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       24.00        24.00        20.98        21.99        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        27.02        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T 
       38.04        42.02        15.02        15.02        32.02        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       26.01        51.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        16.44        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       15.75         0.20        17.82        17.26        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       50.37        83.80        22.36        65.00        62.79        61.41 
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         1.94 
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         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
      102.44        40.34        21.99        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        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.08        11.01        10.06        19.59        11.51 
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         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       13.41        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        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       13.45         1.55        33.67         0.53        35.41       107.67 
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        45.11        39.42        35.93        36.72        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        47.15        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        13.05         8.42         9.70 
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-3599 
       65.98         7.07        36.03        24.00        46.03        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 
        6.05         0.99        15.95        19.99        19.99        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        0.99         0.99        19.99        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       48.03        19.99        36.03         1.02        17.03         0.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       31.00        70.03         1.94        38.96        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        0.69         0.72        26.43        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        78.12         7.17        10.98        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.00        15.02        36.00        10.98        13.05        10.06 
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-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        0.49         2.40        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.34        16.31        11.51        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`7P GAIN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 
       46.65        42.90        24.33        42.28        16.57        37.05 
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-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       61.84         3.02        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       29.00         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       20.98        13.94         6.97         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3821 
       47.01        26.99        19.04        19.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 
        0.00        33.07        36.03        31.07        53.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       12.99        33.01        26.01         2.01        34.03         2.01 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       50.99        13.05        25.02        24.00        19.07         7.96 
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-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        34.98        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        35.01        37.02        39.06         2.96        39.98 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.03        41.00        18.05         0.07        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D 
       10.88         0.46         0.92        27.09        21.44        17.85 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 
        6.77       100.01        11.74         2.24         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        0.33         0.10        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-4746 
       21.14         2.93         2.01       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 
       26.04        30.08        15.02        12.00        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       14.04        12.95        13.05        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 
       13.51        20.19        20.42        18.25        17.85        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       15.58        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HB 
       11.38       119.70       130.65        13.32       140.38       135.65 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
      139.17        26.47        81.37       119.93        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 
       16.24        13.25        19.43         8.35        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       51.75        22.09        26.04        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98        19.33        19.33        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       32.98        31.30        43.04        13.55        19.10        12.72 
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-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 
       20.05         1.02        34.03         2.01        50.04         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         1.02        32.98         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 
       14.01        32.02        28.04        14.04        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        6.02        23.01        37.02        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
       49.97        61.97        41.00         1.45         1.81         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 
        6.97        13.97        15.02        13.97        30.05        12.95 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 
       51.48        32.61        20.55        19.96        17.00        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46        37.51         0.53         1.12 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           131.51            140.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            18.28             19.33 
[1] "0.0 - 131.5 (18.3)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   243 102
  7P GAIN WILD-TYPE 199  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    243  102
  7P GAIN WILD-TYPE  199   60
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON              243               199
  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        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          13         15         57         37       41
  7P GAIN WILD-TYPE        13          6         22         17       20
                   vv
clus                STAGE IVA STAGE IVB
  7P GAIN MUTATED          19         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                97
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III               13                13
  STAGE IIIA              15                 6
  STAGE IIIB              57                22
  STAGE IIIC              37                17
  STAGE IV                41                20
  STAGE IVA               19                 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  61 233  38
  7P GAIN WILD-TYPE   7  46 180  28
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              13                 7
  T2              61                46
  T3             233               180
  T4              38                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7P GAIN MUTATED   167 102  75
  7P GAIN WILD-TYPE 175  47  39
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             167               175
  N1             102                47
  N2              75                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   242  58
  7P GAIN WILD-TYPE 206  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    242   58
  7P GAIN WILD-TYPE  206   28
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             242               206
  1              58                28
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   160 187
  7P GAIN WILD-TYPE 126 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    160  187
  7P GAIN WILD-TYPE  126  135
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             160               126
  MALE               187               135
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                    218                            25
  7P GAIN WILD-TYPE                  163                            35
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                      98                              3
  7P GAIN WILD-TYPE                    48                             10
D13V9, multiclass
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       218               163
  COLON MUCINOUS ADENOCARCINOMA               25                35
  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"
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     7 340
  7P GAIN WILD-TYPE   2 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7  340
  7P GAIN WILD-TYPE    2  259
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                7                 2
  YES             340               259
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   249   4  24  14
  7P GAIN WILD-TYPE 190   1  12  15
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             249               190
  R1               4                 1
  R2              24                12
  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                          40   176
  7P GAIN WILD-TYPE                        20   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                     40                20
  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"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   238  58
  7Q GAIN WILD-TYPE 230  57
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              296               287 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               58                57 
$`7Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
       11.47        11.47        43.76        43.43        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       45.60        13.94        37.25        37.02        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       31.63        30.44        29.19        29.16        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3534 TCGA-AA-3538 TCGA-AA-3542 
       38.99         9.07        36.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       14.01        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 
       61.02        78.08         6.05         2.01        14.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3852 
       35.05         0.99        36.95        37.02        14.93         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3968 
       18.05        31.00        24.00        24.00         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       16.08        34.06        27.02        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T 
       34.03        42.02        15.02        15.02        32.02        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       26.01        51.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96         4.21         0.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
       16.44         0.46        14.50        16.31         0.95         0.20 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 
       17.82        17.26        18.84        75.25        50.37        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        61.41        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         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56       102.44        40.34        21.99        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        27.02        13.02        22.03        22.98        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.08        11.01        10.06        19.59        11.51 
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         7.53        10.13        12.43        14.30        13.41 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-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        13.38        13.45         1.55        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
        0.53        35.41       107.67        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        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.72        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 
       47.15        18.18         9.93        15.65        12.79        13.05 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42         9.70        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-3599 
       65.98         7.07        36.03        24.00        46.03        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 
        0.99        15.95        19.99        19.99        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        0.99        19.99        17.03        35.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 
       19.99        28.04         1.02         0.99        25.97        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-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.96        38.04         0.49         0.69         0.72        26.43 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       10.19         6.05         9.37        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        12.99        12.00        15.02        36.00        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06         5.29        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        0.49        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       16.31        11.51        11.97         9.96        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.39        32.19         0.69         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`7Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        4.80        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5661 
       16.57        37.05        34.65        36.53        14.53        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        27.09         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.39        20.12        19.66        61.84        56.25 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
        3.02        63.98         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       29.00         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 
       20.98        13.94         6.97        54.02         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       47.05        47.01        19.00        26.99        19.04        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-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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       31.07        53.00        17.03         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A 
       26.01        25.02        24.00        19.07         7.96        38.04 
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-A01D 
        0.99        17.03        14.99        21.99        34.98        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        35.01        37.02        39.06         2.96        39.98 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        41.00        18.05         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
        0.72         5.79        10.88         0.92        27.09        15.75 
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-6603 TCGA-AZ-6606 
       32.94         5.13         6.77       100.01        29.56        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.94         2.24         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
        0.10        70.16        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 
       29.06        30.08        15.02        12.00        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       14.04        12.95        13.05        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 
       13.51        20.19        20.42        18.25        17.85        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       15.58        12.39         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D9 
       12.00        11.38       119.70        24.43       130.65       140.38 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
       60.79       117.07        98.24        11.11        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 
       35.87        16.31        29.59        16.24        13.25        19.43 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       28.21         8.35        67.30        53.62        51.75        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       26.04        35.80        26.17        52.80        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       19.33        12.00        42.77        29.46        32.98        31.30 
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        12.72        37.74 
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-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       20.05         1.02        34.03         2.01        50.04         6.05 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         1.02        32.98         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       13.02        14.01        32.02        36.03        14.04        17.03 
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         6.05         6.97         4.73        13.97 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        13.97        30.05        12.95       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 
       37.51         0.66         0.53         1.12        18.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           131.51            140.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           18.115            19.330 
[1] "0.0 - 131.5 (18.1)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   221  86
  7Q GAIN WILD-TYPE 221  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    221   86
  7Q GAIN WILD-TYPE  221   76
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON              221               221
  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       108         7         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          12         10         53         32       37
  7Q GAIN WILD-TYPE        14         11         26         22       24
                   vv
clus                STAGE IVA STAGE IVB
  7Q GAIN MUTATED          18         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               108
  STAGE IIB                3                 7
  STAGE IIC                1                 2
  STAGE III               12                14
  STAGE IIIA              10                11
  STAGE IIIB              53                26
  STAGE IIIC              32                22
  STAGE IV                37                24
  STAGE IVA               18                 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  53 207  34
  7Q GAIN WILD-TYPE   7  54 206  32
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              13                 7
  T2              53                54
  T3             207               206
  T4              34                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
  7Q GAIN MUTATED   151  89  66
  7Q GAIN WILD-TYPE 191  60  48
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             151               191
  N1              89                60
  N2              66                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   211  54
  7Q GAIN WILD-TYPE 237  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    211   54
  7Q GAIN WILD-TYPE  237   32
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             211               237
  1              54                32
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   143 166
  7Q GAIN WILD-TYPE 143 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    143  166
  7Q GAIN WILD-TYPE  143  156
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             143               143
  MALE               166               156
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                    198                            23
  7Q GAIN WILD-TYPE                  183                            37
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                      83                              2
  7Q GAIN WILD-TYPE                    63                             11
D14V9, multiclass
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       198               183
  COLON MUCINOUS ADENOCARCINOMA               23                37
  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"
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5 304
  7Q GAIN WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  304
  7Q GAIN WILD-TYPE    4  295
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                5                 4
  YES             304               295
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   222   3  23  14
  7Q GAIN WILD-TYPE 217   2  13  15
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             222               217
  R1               3                 2
  R2              23                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"
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                          37   154
  7Q GAIN WILD-TYPE                        23   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                     37                23
  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"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   125  33
  8P GAIN WILD-TYPE 343  82
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              158               425 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                82 
$`8P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4107 
       11.47        11.47        24.33        13.94        37.02        32.45 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-A5ZU 
       31.63        29.19        32.71        29.16        24.16         9.63 
TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 
        1.02        35.01         6.97         1.02        36.03        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3558 TCGA-AA-3662 
       29.00        29.00        12.99        14.01        20.98         6.05 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
        6.97        14.01        50.04         5.03        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3870 TCGA-AA-3875 
       10.06        17.03         0.00        31.07        29.98        18.05 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       12.99         2.01        18.05         0.99        17.03        10.98 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 
       51.98         2.96         5.03         0.92         0.07         5.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.42        16.44        27.09        21.44        17.26        18.84 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        61.41        49.41 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 
        5.23         3.19         2.24         3.06         2.14         0.07 
TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
      102.44        51.32         2.01        20.02        37.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
        8.02        27.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6677 TCGA-D5-5541 
       15.02        29.03        14.99        12.99        11.08        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.19        17.75         1.32         4.80        17.13        16.14 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        7.53        12.43        14.30        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
       38.20         7.50        44.32        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6302 
        8.61        13.45         6.18        16.24         8.35        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6626 
       65.85        53.62        44.68        45.11        39.42        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       47.15        18.18        15.65        29.46        32.98         8.42 
TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3574 
       70.03        43.04        12.72        20.02        65.98        36.03 
TCGA-AG-3578 TCGA-AG-3598 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 
       32.02        50.04         1.02        36.95         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
       32.02         1.02         0.99         9.07        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6623 
       64.01        38.04         0.49         0.69         6.05         9.37 
TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        7.17        15.02        13.05        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6810 
        0.49        17.00        16.31        11.51        37.51         0.39 
TCGA-F5-6863 TCGA-G5-6572 
        0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        35.11        45.60        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       37.25        34.65        36.53        14.53        32.91        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        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-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84        56.25         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        3.02        37.05         1.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3548 
        0.00        19.07        34.03        26.01         0.99        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-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        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-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       38.99        36.95        37.02        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        24.03        27.02        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-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-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-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       18.05        38.04         4.01        27.02        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01        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-6901 
       21.37         4.21        56.55         0.79         0.72        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.95        15.75         0.20        17.82        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41         5.65        83.80 
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 
        1.94         3.25         3.29         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56        40.34        70.16        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.14         2.93       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        16.01 
TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
        5.03        12.00        14.04        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 
       13.51        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        12.39        10.13         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D0 
       11.64        13.41         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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.64        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        35.41        19.43       107.67        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        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        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        52.80        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        13.05        12.00        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30         9.70        30.28        24.13        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
       15.39        10.39        86.63        11.84        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-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       19.99        19.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        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         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        6.97         4.73        13.97        78.12        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        12.00        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       30.05        12.95        10.06         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         0.46        18.28        55.76        26.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           119.70            140.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            17.08             19.99 
[1] "0.0 - 119.7 (17.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   128  40
  8P GAIN WILD-TYPE 314 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    128   40
  8P GAIN WILD-TYPE  314  122
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON              128               314
  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        47         3         2
  8P GAIN WILD-TYPE      76        1       22       124         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           4          3         22         16       20
  8P GAIN WILD-TYPE        22         18         57         38       41
                   vv
clus                STAGE IVA STAGE IVB
  8P GAIN MUTATED           6         0
  8P GAIN WILD-TYPE        21         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               47               124
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III                4                22
  STAGE IIIA               3                18
  STAGE IIIB              22                57
  STAGE IIIC              16                38
  STAGE IV                20                41
  STAGE IVA                6                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
  8P GAIN MUTATED     5  27 118  17
  8P GAIN WILD-TYPE  15  80 295  49
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               5                15
  T2              27                80
  T3             118               295
  T4              17                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
  8P GAIN MUTATED   101  34  32
  8P GAIN WILD-TYPE 241 115  82
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             101               241
  N1              34               115
  N2              32                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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   119  27
  8P GAIN WILD-TYPE 329  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    119   27
  8P GAIN WILD-TYPE  329   59
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             119               329
  1              27                59
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    80  88
  8P GAIN WILD-TYPE 206 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     80   88
  8P GAIN WILD-TYPE  206  234
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              80               206
  MALE                88               234
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                    113                            15
  8P GAIN WILD-TYPE                  268                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                      36                              3
  8P GAIN WILD-TYPE                   110                             10
D15V9, multiclass
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       113               268
  COLON MUCINOUS ADENOCARCINOMA               15                45
  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"
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3 165
  8P GAIN WILD-TYPE   6 434
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3  165
  8P GAIN WILD-TYPE    6  434
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                3                 6
  YES             165               434
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   112   0  14  12
  8P GAIN WILD-TYPE 327   5  22  17
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             112               327
  R1               0                 5
  R2              14                22
  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                          18    90
  8P GAIN WILD-TYPE                        42   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                     18                42
  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"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   234  61
  8Q GAIN WILD-TYPE 234  54
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              295               288 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               61                54 
$`8Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 
       11.47        11.47        43.43        24.33        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       13.94        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       31.63        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        24.16        24.69        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         5.03         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        6.97         1.02        36.03        19.07         0.00        29.00 
TCGA-AA-3534 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-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        20.98        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
        5.98        37.05        36.00         5.03        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3856 
       10.06        36.95        37.02        17.03         0.00         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-3930 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
        2.01        12.99        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       26.01        24.00        13.94        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z 
       17.03        10.98        12.00        31.00         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
       51.98         2.96         5.03         0.92        41.00         0.07 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
        4.21         5.79        27.42        16.44         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 
       16.31        21.44        17.26        18.84        75.25        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        61.41        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.06         2.14         0.07         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
      102.44        15.62        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       25.02         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6676 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       11.08        13.51        11.51        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G 
      140.38         7.50        44.32         6.12        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
        6.18        16.31        16.24         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       67.30        65.85        53.62        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       39.42        35.93        36.00        26.43        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW 
       18.18        10.98         9.93        15.65        12.00        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42        30.28        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        12.72        37.74        10.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       20.02        10.39        65.98        36.03        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       24.00         1.02        46.03        50.04         6.05         0.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3887 TCGA-AG-3896 
       19.99         7.99         1.02        32.98        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-4022 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
        0.99        25.97        37.02        15.95         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 
       31.00        70.03        64.01        51.98         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        0.49         1.45         0.69        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        4.73        78.12         7.17        12.99        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 
       24.13        32.61         0.49        17.00        16.34        16.31 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       11.51        10.78        13.64         9.96        37.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.39        32.19         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       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 
       15.02        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-6196 TCGA-AY-6386 
        0.46        14.50         0.95        15.75         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33        50.37        58.39         1.41         5.65 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
       62.79         6.77       100.01         3.25         3.29         0.26 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 
        0.33        17.56        40.34        70.16        49.08        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 
       21.14         2.93       124.27        23.05        26.04        22.03 
TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 
       16.01        12.00        14.04        16.04        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6532 
       12.03        45.40        12.26        19.59        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       17.85        12.49        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA 
       12.00        92.75        49.91        13.32        12.59       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-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
      119.93        95.18        11.11        35.87         1.55        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       28.21        82.39        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V 
       13.78        35.80        26.17        91.79        52.80        19.33 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D 
       19.33        12.79        13.05        42.77        31.30         9.70 
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-3727 TCGA-AG-3728 TCGA-AG-3742 
       12.03        15.95        19.99         0.99        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.01        19.99        36.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       23.01        36.03        12.00        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97        41.00         0.72        26.43         1.81         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
        6.97        13.97        10.98        11.01        15.02        12.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00        30.05        12.95         5.29       129.27        51.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       17.69        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
       31.30         0.66         0.69         0.53         1.12        18.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           140.38            139.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.05             19.51 
[1] "0.0 - 140.4 (18.1)" "0.0 - 139.2 (19.5)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   223  87
  8Q GAIN WILD-TYPE 219  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    223   87
  8Q GAIN WILD-TYPE  219   75
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON              223               219
  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        84         3         2
  8Q GAIN WILD-TYPE      59        1       15        87         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          11         13         39         33       42
  8Q GAIN WILD-TYPE        15          8         40         21       19
                   vv
clus                STAGE IVA STAGE IVB
  8Q GAIN MUTATED          13         0
  8Q GAIN WILD-TYPE        14         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               84                87
  STAGE IIB                3                 7
  STAGE IIC                2                 1
  STAGE III               11                15
  STAGE IIIA              13                 8
  STAGE IIIB              39                40
  STAGE IIIC              33                21
  STAGE IV                42                19
  STAGE IVA               13                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
  8Q GAIN MUTATED     6  53 219  32
  8Q GAIN WILD-TYPE  14  54 194  34
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               6                14
  T2              53                54
  T3             219               194
  T4              32                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   166  74  69
  8Q GAIN WILD-TYPE 176  75  45
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             166               176
  N1              74                75
  N2              69                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   219  55
  8Q GAIN WILD-TYPE 229  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    219   55
  8Q GAIN WILD-TYPE  229   31
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             219               229
  1              55                31
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   145 166
  8Q GAIN WILD-TYPE 141 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    145  166
  8Q GAIN WILD-TYPE  141  156
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             145               141
  MALE               166               156
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                    199                            23
  8Q GAIN WILD-TYPE                  182                            37
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                      81                              4
  8Q GAIN WILD-TYPE                    65                              9
D16V9, multiclass
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       199               182
  COLON MUCINOUS ADENOCARCINOMA               23                37
  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"
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     8 303
  8Q GAIN WILD-TYPE   1 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8  303
  8Q GAIN WILD-TYPE    1  296
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                8                 1
  YES             303               296
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   212   3  26  17
  8Q GAIN WILD-TYPE 227   2  10  12
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             212               227
  R1               3                 2
  R2              26                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                          32   157
  8Q GAIN WILD-TYPE                        28   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                     32                28
  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"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    81  32
  9P GAIN WILD-TYPE 387  83
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              113               470 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               32                83 
$`9P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-6142 
       43.76        44.91        13.94        37.02        31.63        25.08 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3520 TCGA-AA-3532 
       20.28        16.24        56.25         5.03        24.03        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 
       29.00        14.01        33.99        20.98        78.08         6.97 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3854 
        2.01        50.04        14.93        10.06         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3976 TCGA-AA-3994 TCGA-AA-A00Q TCGA-AA-A00Z 
        0.99        27.02        26.01        27.02        42.02        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       15.02        10.98        51.98         5.79        22.42        16.44 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-6600 TCGA-AZ-6603 
       15.75         0.20        17.26        50.37        12.10        29.56 
TCGA-CA-5796 TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        3.25        21.99        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        14.04        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        13.41        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        13.38 
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        13.05        42.77         9.70        70.03        39.48 
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       17.23        12.72        20.02        46.03         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3890 TCGA-AG-3896 
        0.99        19.99         7.99         0.99        17.03         1.02 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 
       32.02        36.03        70.03        10.98        51.98        38.04 
TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 
        0.69         0.72        10.98        36.00       129.27         2.40 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6810 
       11.51        10.78         8.45         9.96        28.57         0.39 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         1.12         0.46        18.28        26.43 

$`9P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        45.60        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A566 TCGA-A6-A567 
       24.39        23.87        20.12        19.66        24.92        61.84 
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-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-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-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-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        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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         4.21        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        75.25        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        61.41        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        16.01        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-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44         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-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64        13.45        35.87        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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        47.15        52.80 
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        12.00 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 
       29.46        32.98         8.42        31.30        30.28        24.13 
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-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        15.39        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-3593 TCGA-AG-3599 TCGA-AG-3600 
       20.05        24.00         1.02        34.03        12.03         6.05 
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         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       14.01        48.03        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        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-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        31.00        64.01        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       61.97        41.00         0.49         1.45        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         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.97        78.12         7.17        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.00        13.97        15.02        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
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-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.31        16.41         8.61        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
       37.51        31.30        32.19         0.66         0.53         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            140.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            16.24             19.81 
[1] "0.0 - 129.3 (16.2)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    79  42
  9P GAIN WILD-TYPE 363 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     79   42
  9P GAIN WILD-TYPE  363  120
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON               79               363
  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       140         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           3          8         11         18       11
  9P GAIN WILD-TYPE        23         13         68         36       50
                   vv
clus                STAGE IVA STAGE IVB
  9P GAIN MUTATED           7         1
  9P GAIN WILD-TYPE        20         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               140
  STAGE IIB                2                 8
  STAGE IIC                2                 1
  STAGE III                3                23
  STAGE IIIA               8                13
  STAGE IIIB              11                68
  STAGE IIIC              18                36
  STAGE IV                11                50
  STAGE IVA                7                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
  9P GAIN MUTATED     3  17  84  16
  9P GAIN WILD-TYPE  17  90 329  50
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               3                17
  T2              17                90
  T3              84               329
  T4              16                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
  9P GAIN MUTATED    61  31  28
  9P GAIN WILD-TYPE 281 118  86
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              61               281
  N1              31               118
  N2              28                86
[1] 3 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  18
  9P GAIN WILD-TYPE 363  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     85   18
  9P GAIN WILD-TYPE  363   68
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              85               363
  1              18                68
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    59  62
  9P GAIN WILD-TYPE 227 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     59   62
  9P GAIN WILD-TYPE  227  260
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              59               227
  MALE                62               260
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                     61                            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
D17V9, multiclass
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        61               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"
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1 120
  9P GAIN WILD-TYPE   8 479
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1  120
  9P GAIN WILD-TYPE    8  479
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 8
  YES             120               479
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    94   0   6   3
  9P GAIN WILD-TYPE 345   5  30  26
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              94               345
  R1               0                 5
  R2               6                30
  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                          17    55
  9P GAIN WILD-TYPE                        43   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                     17                43
  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"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    66  28
  9Q GAIN WILD-TYPE 402  87
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               94               489 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28                87 
$`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-6196 TCGA-AY-A54L 
        5.79        22.42        16.44        15.75         0.20        17.26 
TCGA-AZ-4313 TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-5914 TCGA-CM-5862 TCGA-CM-5864 
       50.37        12.10         3.25        21.99         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-6531 TCGA-D5-6539 
       17.03        14.04        29.03        14.99        17.75        12.49 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A288 
       11.64        13.41        12.59         7.50         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6323 
       26.47        98.24        95.18        13.38         6.18        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QL-A97D 
       91.79        46.75        10.98        12.79        13.05         9.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3598 
       70.03        39.48        12.72        20.02         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3878 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 
        0.99         0.99        17.03         1.02        32.02        10.98 
TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE 
       51.98        38.04         0.72        10.98        36.00       129.27 
TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 
        2.40        11.51        10.78         9.96         0.39         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        1.12         0.46        18.28        26.43 

$`9Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        45.60        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        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-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-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-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3552 
       34.03        26.01        12.99         0.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       19.99        61.02         6.05        54.02        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-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-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.00        33.07        32.05        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-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-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07         7.96        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-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        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-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-6963 TCGA-AD-6964 
        4.21        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-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
        0.95        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        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 
       83.80        22.36        65.00        62.79        61.41        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-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        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-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-D5-6532 
       19.59        13.51        11.51        20.19        20.42        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-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.76       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
      117.07         8.61        11.11        13.64        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       36.72        36.00        26.43        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        47.15        52.80        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
        8.42        31.30        30.28        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       15.39        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-3593 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02        46.03        34.03        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       13.02        35.01        14.01        48.03        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         0.99        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 
        0.49         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         6.05         6.97         9.37         4.73        13.97 
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        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        15.02        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         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 
       37.51        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            140.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            14.96             19.99 
[1] "0.0 - 129.3 (15.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    69  32
  9Q GAIN WILD-TYPE 373 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     69   32
  9Q GAIN WILD-TYPE  373  130
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON               69               373
  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       142         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           3          6          8         14       11
  9Q GAIN WILD-TYPE        23         15         71         40       50
                   vv
clus                STAGE IVA STAGE IVB
  9Q GAIN MUTATED           4         1
  9Q GAIN WILD-TYPE        23         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               142
  STAGE IIB                1                 9
  STAGE IIC                2                 1
  STAGE III                3                23
  STAGE IIIA               6                15
  STAGE IIIB               8                71
  STAGE IIIC              14                40
  STAGE IV                11                50
  STAGE IVA                4                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
  9Q GAIN MUTATED     3  13  71  13
  9Q GAIN WILD-TYPE  17  94 342  53
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               3                17
  T2              13                94
  T3              71               342
  T4              13                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
  9Q GAIN MUTATED    54  23  23
  9Q GAIN WILD-TYPE 288 126  91
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              54               288
  N1              23               126
  N2              23                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"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    71  16
  9Q GAIN WILD-TYPE 377  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     71   16
  9Q GAIN WILD-TYPE  377   70
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              71               377
  1              16                70
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    46  55
  9Q GAIN WILD-TYPE 240 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     46   55
  9Q GAIN WILD-TYPE  240  267
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              46               240
  MALE                55               267
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                     53                            16
  9Q GAIN WILD-TYPE                  328                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                      27                              4
  9Q GAIN WILD-TYPE                   119                              9
D18V9, multiclass
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        53               328
  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"
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1 100
  9Q GAIN WILD-TYPE   8 499
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1  100
  9Q GAIN WILD-TYPE    8  499
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 8
  YES             100               499
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    77   0   6   3
  9Q GAIN WILD-TYPE 362   5  30  26
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              77               362
  R1               0                 5
  R2               6                30
  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                        45   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                45
  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"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    30  13
  10P GAIN WILD-TYPE 438 102
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                43                540 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                102 
$`10P GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6650 
       11.47        43.76        37.02        32.45        24.16        20.61 
TCGA-A6-6782 TCGA-AA-3548 TCGA-AA-3666 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3869 
       20.28        33.99         2.01         0.00        33.07        27.02 
TCGA-AA-3952 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 TCGA-CM-5860 
        2.01        16.31        17.26        18.84         2.24        16.01 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6534 
        5.03        14.04        11.01        19.59        13.51        43.27 
TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6299 
       14.30        12.59         7.50         8.61         1.55        74.56 
TCGA-G4-6317 TCGA-G4-6625 TCGA-QL-A97D TCGA-AF-2689 TCGA-AG-3902 TCGA-AG-A014 
       36.00        91.79         9.70        39.48        32.02        15.95 
TCGA-AG-A016 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 TCGA-DY-A1DF TCGA-F5-6571 
        9.07        70.03        10.19        10.98        24.13        31.30 
TCGA-F5-6812 
        0.66 

$`10P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        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-3667 
       61.02        78.08         6.05         6.97        54.02        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-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-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       37.02        14.93        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-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-3955 
       12.99        24.00        33.01        26.01        24.00        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 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21 
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-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        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        75.25        50.37        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        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         1.94         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         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        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        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.26        11.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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        47.15        52.80        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        13.05        12.00 
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-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 
       12.72        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-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        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         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
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 
        0.49         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         6.05         6.97         9.37         4.73        13.97 
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        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         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-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        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39        32.19         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         0.46        18.28        55.76        47.08        26.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             91.79             140.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            16.310             19.215 
[1] "0.0 - 91.8 (16.3)"  "0.0 - 140.4 (19.2)"
[1] "hr=" "1.8"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    36  11
  10P GAIN WILD-TYPE 406 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     36   11
  10P GAIN WILD-TYPE  406  151
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON                36                406
  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        15         1         0
  10P GAIN WILD-TYPE      99        1       35       156         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           2          1          5          8        5
  10P GAIN WILD-TYPE        24         20         74         46       56
                    vv
clus                 STAGE IVA STAGE IVB
  10P GAIN MUTATED           3         0
  10P GAIN WILD-TYPE        24         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                15                156
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                1                 20
  STAGE IIIB                5                 74
  STAGE IIIC                8                 46
  STAGE IV                  5                 56
  STAGE IVA                 3                 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
  10P GAIN MUTATED     1   4  38   4
  10P GAIN WILD-TYPE  19 103 375  62
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 19
  T2                4                103
  T3               38                375
  T4                4                 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
  10P GAIN MUTATED    22   9  16
  10P GAIN WILD-TYPE 320 140  98
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               22                320
  N1                9                140
  N2               16                 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"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    31   8
  10P GAIN WILD-TYPE 417  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     31    8
  10P GAIN WILD-TYPE  417   78
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               31                417
  1                8                 78
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    23  24
  10P GAIN WILD-TYPE 263 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     23   24
  10P GAIN WILD-TYPE  263  298
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               23                263
  MALE                 24                298
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                     32                             4
  10P GAIN WILD-TYPE                  349                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                      11                              0
  10P GAIN WILD-TYPE                   135                             13
D19V9, multiclass
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         32                349
  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"
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  46
  10P GAIN WILD-TYPE   8 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   46
  10P GAIN WILD-TYPE    8  553
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 1                  8
  YES               46                553
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    34   1   3   2
  10P GAIN WILD-TYPE 405   4  33  27
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               34                405
  R1                1                  4
  R2                3                 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"
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                           6    26
  10P GAIN WILD-TYPE                        54   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                       6                 54
  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"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    20   5
  10Q GAIN WILD-TYPE 448 110
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                25                558 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                110 
$`10Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-4107 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3982 
       11.47        32.45         2.01        33.07        27.02        27.02 
TCGA-AA-A01R TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-6678 
       35.01        17.26        18.84         2.24        16.01        11.01 
TCGA-D5-5539 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6704 TCGA-G4-6299 
       19.59        14.30        12.59         7.50         1.55        74.56 
TCGA-G4-6317 TCGA-QL-A97D TCGA-AF-2689 TCGA-AG-3999 TCGA-AG-A01W TCGA-BM-6198 
       36.00         9.70        39.48        28.04        70.03        10.19 
TCGA-DC-4745 
       10.98 

$`10Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        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-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 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-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-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-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-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-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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         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         4.21 
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-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        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        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        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         1.94 
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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        13.51        11.51 
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         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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        47.15        52.80        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        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        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        12.72        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-3593 TCGA-AG-3594 
       20.05        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-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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-4022 
       19.99        36.03        14.04         1.02        17.03         0.99 
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-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         0.49         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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.73        13.97        78.12         7.17        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         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        37.51        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         0.46        18.28        55.76        47.08        26.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.55               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             74.56             140.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            17.260             19.085 
[1] "1.6 - 74.6 (17.3)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    21   6
  10Q GAIN WILD-TYPE 421 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     21    6
  10Q GAIN WILD-TYPE  421  156
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON                21                421
  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         6         0         0
  10Q GAIN WILD-TYPE     101        1       35       165        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          1          4          5        2
  10Q GAIN WILD-TYPE        24         20         75         49       59
                    vv
clus                 STAGE IVA STAGE IVB
  10Q GAIN MUTATED           2         0
  10Q GAIN WILD-TYPE        25         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                 6                165
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                1                 20
  STAGE IIIB                4                 75
  STAGE IIIC                5                 49
  STAGE IV                  2                 59
  STAGE IVA                 2                 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
  10Q GAIN MUTATED     0   3  22   2
  10Q GAIN WILD-TYPE  20 104 391  64
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                 20
  T2                3                104
  T3               22                391
  T4                2                 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
  10Q GAIN MUTATED    10   8   9
  10Q GAIN WILD-TYPE 332 141 105
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               10                332
  N1                8                141
  N2                9                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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    16   4
  10Q GAIN WILD-TYPE 432  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     16    4
  10Q GAIN WILD-TYPE  432   82
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               16                432
  1                4                 82
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    14  13
  10Q GAIN WILD-TYPE 272 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   13
  10Q GAIN WILD-TYPE  272  309
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                272
  MALE                 13                309
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                     17                             4
  10Q GAIN WILD-TYPE                  364                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                       6                              0
  10Q GAIN WILD-TYPE                   140                             13
D20V9, multiclass
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         17                364
  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"
D20V10, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  26
  10Q GAIN WILD-TYPE   8 573
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   26
  10Q GAIN WILD-TYPE    8  573
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                  8
  YES               26                573
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    20   0   1   2
  10Q GAIN WILD-TYPE 419   5  35  27
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               20                419
  R1                0                  5
  R2                1                 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"
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                           4    13
  10Q GAIN WILD-TYPE                        56   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                       4                 56
  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"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    64  16
  11P GAIN WILD-TYPE 404  99
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                80                503 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                 99 
$`11P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 
       43.76        43.43        44.91        29.19        25.08        25.18 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3542 TCGA-AA-3552 
       23.87        56.25         5.03         1.02        12.99        13.02 
TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 
       24.00        19.99        50.04        37.02        17.03        33.07 
TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F 
        0.99        24.03        18.05        20.98        27.02        34.03 
TCGA-AA-A02F TCGA-AD-6888 TCGA-AD-6901 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK 
       39.98         4.21        22.42        16.31         0.95        18.84 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CK-4948 TCGA-CM-4750 
       65.00        62.79        29.56         1.94       102.44         8.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6536 
       17.03        29.03        21.99        11.08         1.32        17.85 
TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 
        7.53        13.41        49.91        35.97        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6314 TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-3913 
       45.11        35.93        29.46        30.28        17.23        10.39 
TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3612 
       20.02        65.98        12.00        46.03        19.99        19.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 
       36.03         1.02        25.97        31.00        26.43        10.19 
TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        9.37         4.73        11.01        12.99        12.00        36.00 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 
       30.05       126.44         2.40        16.31        13.64         0.39 
TCGA-F5-6811 TCGA-G5-6233 
       32.19        18.28 

$`11P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        42.28        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-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        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-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       61.84         9.63         7.04         3.02        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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
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-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-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-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       14.93         0.00        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
        2.96         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-6889 
       39.98        18.05        40.96         0.07        21.37        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-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       16.44         0.46         0.92        14.50        27.09        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01         5.23        11.74         3.19         2.24 
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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10         1.35        17.56        40.34        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        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        14.04        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        13.51        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         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-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-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        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        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        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        35.41        19.43       107.67        28.21 
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-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        51.75        39.42        36.72        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        47.15        52.80        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        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       42.77        32.98         8.42        31.30         9.70        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        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        14.50        16.83        15.39        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-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 
       12.03         6.05         0.99        15.95         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         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-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       17.03         0.99        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         0.49         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         6.05         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       13.97        78.12         7.17        10.98        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        12.95        13.05        10.06         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        37.51 
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         0.46        55.76        47.08        26.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            126.44             140.38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            22.205             18.280 
[1] "0.4 - 126.4 (22.2)" "0.0 - 140.4 (18.3)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    52  31
  11P GAIN WILD-TYPE 390 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     52   31
  11P GAIN WILD-TYPE  390  131
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON                52                390
  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       153         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0          5         13         10       12
  11P GAIN WILD-TYPE        26         16         66         44       49
                    vv
clus                 STAGE IVA STAGE IVB
  11P GAIN MUTATED           6         0
  11P GAIN WILD-TYPE        21         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                153
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 0                 26
  STAGE IIIA                5                 16
  STAGE IIIB               13                 66
  STAGE IIIC               10                 44
  STAGE IV                 12                 49
  STAGE IVA                 6                 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
  11P GAIN MUTATED     4  17  59   4
  11P GAIN WILD-TYPE  16  90 354  62
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 16
  T2               17                 90
  T3               59                354
  T4                4                 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
  11P GAIN MUTATED    40  22  21
  11P GAIN WILD-TYPE 302 127  93
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               40                302
  N1               22                127
  N2               21                 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"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    56  18
  11P GAIN WILD-TYPE 392  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     56   18
  11P GAIN WILD-TYPE  392   68
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               56                392
  1               18                 68
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    39  45
  11P GAIN WILD-TYPE 247 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     39   45
  11P GAIN WILD-TYPE  247  277
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               39                247
  MALE                 45                277
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                     50                             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
D21V9, multiclass
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         50                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"
D21V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3  81
  11P GAIN WILD-TYPE   6 518
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   81
  11P GAIN WILD-TYPE    6  518
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 3                  6
  YES               81                518
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    59   1   6   2
  11P GAIN WILD-TYPE 380   4  30  27
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               59                380
  R1                1                  4
  R2                6                 30
  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                          10    46
  11P GAIN WILD-TYPE                        50   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                      10                 50
  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"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    62  12
  11Q GAIN WILD-TYPE 406 103
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                509 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                103 
$`11Q GAIN MUTATED`
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6648 
       43.43        44.91        29.19        29.16        25.08        25.18 
TCGA-A6-A56B TCGA-AA-3494 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 
       56.25         1.02        29.00        12.99        13.02        24.00 
TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       19.99        50.04        37.05        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3955 TCGA-AA-3982 
       33.07         0.99        31.07        24.03        20.98        27.02 
TCGA-AA-A00F TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       34.03        16.31        18.84        65.00        62.79        29.56 
TCGA-AZ-6608 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 
        1.94       102.44         8.02        17.03        29.03        21.99 
TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D8 
       11.08        11.51         1.32         7.53        13.41        12.59 
TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 TCGA-QG-A5YW 
       35.97        65.85        55.04        45.11        35.93        29.46 
TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 
       30.28        17.23        10.39        65.98        12.00        46.03 
TCGA-AG-3612 TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N 
       19.99         1.02        36.03         1.02        25.97        31.00 
TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       26.43         9.37         4.73        11.01        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 
       15.02        36.00       126.44        16.31        13.64         0.39 
TCGA-F5-6811 TCGA-F5-6812 
       32.19         0.66 

$`11Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        42.28        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       16.57        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-A6-5661 
       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-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        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-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-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        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-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-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-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-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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        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-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 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21 
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-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33        75.25        50.37        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        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        13.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        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-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-A28G 
        6.12        14.04        26.47        81.37       119.93        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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        67.30        53.62        44.68        51.75        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        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        47.15        52.80 
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-A5YX TCGA-QG-A5Z1 
       12.79        13.05        12.00        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       31.30         9.70        70.03        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        12.72        37.74        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        10.39        86.63        11.84        36.03 
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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        1.02        32.98         0.99         0.99        19.99        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-4005 TCGA-AG-4008 TCGA-AG-4022 
       32.02        19.99        28.04        14.04        17.03         0.99 
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-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        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         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        1.81        10.19         6.05         6.05         6.97        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        10.98        15.02        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06         5.29        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-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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       31.30        28.57         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            126.44             140.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            24.015             19.000 
[1] "0.4 - 126.4 (24.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    50  26
  11Q GAIN WILD-TYPE 392 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     50   26
  11Q GAIN WILD-TYPE  392  136
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON                50                392
  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       156         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          4         12         10        9
  11Q GAIN WILD-TYPE        26         17         67         44       52
                    vv
clus                 STAGE IVA STAGE IVB
  11Q GAIN MUTATED           7         0
  11Q GAIN WILD-TYPE        20         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                156
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                4                 17
  STAGE IIIB               12                 67
  STAGE IIIC               10                 44
  STAGE IV                  9                 52
  STAGE IVA                 7                 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
  11Q GAIN MUTATED     2  16  53   5
  11Q GAIN WILD-TYPE  18  91 360  61
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 18
  T2               16                 91
  T3               53                360
  T4                5                 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
  11Q GAIN MUTATED    36  21  19
  11Q GAIN WILD-TYPE 306 128  95
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               36                306
  N1               21                128
  N2               19                 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"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    51  16
  11Q GAIN WILD-TYPE 397  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     51   16
  11Q GAIN WILD-TYPE  397   70
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               51                397
  1               16                 70
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    36  40
  11Q GAIN WILD-TYPE 250 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     36   40
  11Q GAIN WILD-TYPE  250  282
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               36                250
  MALE                 40                282
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                     49                             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
D22V9, multiclass
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         49                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"
D22V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2  74
  11Q GAIN WILD-TYPE   7 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2   74
  11Q GAIN WILD-TYPE    7  525
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 2                  7
  YES               74                525
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    55   1   4   2
  11Q GAIN WILD-TYPE 384   4  32  27
D22V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               55                384
  R1                1                  4
  R2                4                 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"
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                          10    39
  11Q GAIN WILD-TYPE                        50   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                      10                 50
  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"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    90  28
  12P GAIN WILD-TYPE 378  87
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               118                465 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                 87 
$`12P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
       11.47        11.47        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-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 
        0.92         0.20        18.84         5.13        49.41         6.77 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 
        3.19         1.94         2.24         3.06       102.44        40.34 
TCGA-CK-4952 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 
       15.62        20.02        25.02        16.01        15.02        21.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 
       13.02        14.04        11.01        20.19        17.75         4.80 
TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30        11.64        13.41        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6306 
       24.43        44.32        95.18         8.61        35.87        44.68 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-AF-3400 TCGA-AF-3911 
       13.78        47.15        10.98        15.65        12.72        37.74 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 
       16.83        10.39        36.03        46.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 
       19.99         7.99         1.02        36.95         1.02        36.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 TCGA-DC-6682 
       15.95        36.03        38.96        61.97        78.12        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 
       10.06         5.29       126.44        32.61        19.96        18.28 
TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
       17.69        13.64        11.97        18.28 

$`12P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       24.33        42.28        35.11        45.60        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        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-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02        37.05         1.02        35.01        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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         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-3561 
       24.00        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 
       14.01        50.04        47.05        47.01        15.02        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       36.00        85.05        19.04        10.06        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        36.95        17.03        10.06 
TCGA-AA-3850 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-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01         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-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        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-A02W TCGA-AA-A03F 
        2.96        39.98         2.01         5.03        41.00        18.05 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        10.88         0.20        16.44         0.46        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        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       11.74         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 
        0.33         0.10         1.35        17.56        70.16        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       23.05        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        14.04        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        13.51        11.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04         9.44         1.51        11.38        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-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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
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-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        12.79        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30         9.70        30.28        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-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       10.39        14.50        15.39        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       20.05        24.00         1.02        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        19.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 
       32.98         0.99         0.99        19.99        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02         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-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        41.00        38.04         0.49         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 
        6.05         6.97         9.37         4.73        13.97         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC 
       15.02        36.00        10.98        30.05        12.95        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-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.55        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-7004 
       16.41         8.61        11.51        10.78        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        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         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  0 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            126.44             140.38 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             17.90              19.33 
[1] "0.0 - 126.4 (17.9)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.4"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    94  33
  12P GAIN WILD-TYPE 348 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     94   33
  12P GAIN WILD-TYPE  348  129
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON                94                348
  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       126         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           4          5          9         12       11
  12P GAIN WILD-TYPE        22         16         70         42       50
                    vv
clus                 STAGE IVA STAGE IVB
  12P GAIN MUTATED           7         0
  12P GAIN WILD-TYPE        20         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                126
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 4                 22
  STAGE IIIA                5                 16
  STAGE IIIB                9                 70
  STAGE IIIC               12                 42
  STAGE IV                 11                 50
  STAGE IVA                 7                 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
  12P GAIN MUTATED     1  24  87  14
  12P GAIN WILD-TYPE  19  83 326  52
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                 19
  T2               24                 83
  T3               87                326
  T4               14                 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
  12P GAIN MUTATED    81  24  22
  12P GAIN WILD-TYPE 261 125  92
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               81                261
  N1               24                125
  N2               22                 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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    94  16
  12P GAIN WILD-TYPE 354  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     94   16
  12P GAIN WILD-TYPE  354   70
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               94                354
  1               16                 70
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    60  67
  12P GAIN WILD-TYPE 226 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     60   67
  12P GAIN WILD-TYPE  226  255
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               60                226
  MALE                 67                255
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                     80                            14
  12P GAIN WILD-TYPE                  301                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                      28                              4
  12P GAIN WILD-TYPE                   118                              9
D23V9, multiclass
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         80                301
  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"
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3 124
  12P GAIN WILD-TYPE   6 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3  124
  12P GAIN WILD-TYPE    6  475
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 3                  6
  YES              124                475
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    94   1   5   6
  12P GAIN WILD-TYPE 345   4  31  23
D23V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               94                345
  R1                1                  4
  R2                5                 31
  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                        49   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                 49
  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"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    81  23
  12Q GAIN WILD-TYPE 387  92
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               104                479 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                 92 
$`12Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
       11.47        11.47        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         1.94         2.24 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4747 TCGA-CM-5860 
        3.06       102.44        40.34        15.62        25.02        16.01 
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        13.64        35.87 
TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D 
       44.68        13.78        47.15        10.98        15.65         9.70 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3883 
       12.72        16.83        36.03         2.01        19.99         1.02 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-DC-6682 
        1.02        36.03        36.03        38.96        61.97        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       10.06       126.44        32.61        19.96        18.28        17.69 
TCGA-EI-6885 TCGA-EI-7002 
       13.64        11.97 

$`12Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       24.33        42.28        35.11        45.60        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        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-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02        37.05         1.02        35.01        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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         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-3561 
       24.00        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 
       19.00        36.00        85.05        19.04        10.06        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        36.95        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-3947 TCGA-AA-3952 TCGA-AA-3955 
       18.05        31.00         2.01        33.01         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-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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-A02W TCGA-AA-A03F TCGA-AD-6548 
       39.98         2.01         5.03        41.00        18.05        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        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-AU-3779 
       27.42        10.88         0.20        16.44         0.46        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        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        75.25        50.37 
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        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        65.00        62.79        61.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 
       29.56         5.23        11.74         3.19         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         0.26         0.33         0.10         1.35 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41         1.51        11.38        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-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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
        8.61        13.38        11.11        13.45         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        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 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       23.51        74.56        67.30        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        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-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        52.80        18.18        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        30.28        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-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       20.05        24.00         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        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         1.02        32.98         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-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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        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-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-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        41.00        38.04         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        36.00        10.98        30.05        12.95         5.29 
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-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
        2.40        20.55        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        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 
        0.46        18.28        55.76        47.08        26.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  0 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            126.44             140.38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            18.165             19.330 
[1] "0.0 - 126.4 (18.2)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    88  23
  12Q GAIN WILD-TYPE 354 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     88   23
  12Q GAIN WILD-TYPE  354  139
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON                88                354
  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       126         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           3          6          9          8        6
  12Q GAIN WILD-TYPE        23         15         70         46       55
                    vv
clus                 STAGE IVA STAGE IVB
  12Q GAIN MUTATED           7         0
  12Q GAIN WILD-TYPE        20         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                126
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                6                 15
  STAGE IIIB                9                 70
  STAGE IIIC                8                 46
  STAGE IV                  6                 55
  STAGE IVA                 7                 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
  12Q GAIN MUTATED     1  22  75  12
  12Q GAIN WILD-TYPE  19  85 338  54
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                 19
  T2               22                 85
  T3               75                338
  T4               12                 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
  12Q GAIN MUTATED    75  25  11
  12Q GAIN WILD-TYPE 267 124 103
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               75                267
  N1               25                124
  N2               11                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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    86  12
  12Q GAIN WILD-TYPE 362  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     86   12
  12Q GAIN WILD-TYPE  362   74
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               86                362
  1               12                 74
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    56  55
  12Q GAIN WILD-TYPE 230 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     56   55
  12Q GAIN WILD-TYPE  230  267
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               56                230
  MALE                 55                267
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                     73                            15
  12Q GAIN WILD-TYPE                  308                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                      20                              2
  12Q GAIN WILD-TYPE                   126                             11
D24V9, multiclass
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         73                308
  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"
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1 110
  12Q GAIN WILD-TYPE   8 489
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1  110
  12Q GAIN WILD-TYPE    8  489
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  8
  YES              110                489
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    85   1   4   4
  12Q GAIN WILD-TYPE 354   4  32  25
D24V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               85                354
  R1                1                  4
  R2                4                 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"
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                        48   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                 48
  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"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   283  67
  13Q GAIN WILD-TYPE 185  48
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               350                233 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                67                 48 
$`13Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
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-A6-3807 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-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       21.76        24.69        23.87        20.28        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         7.04        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        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-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       19.99        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 
       15.02         5.98        37.05        19.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       10.06        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        32.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3949 
       24.03        27.02        29.98         2.01        12.99        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
       20.98        34.03        16.08        50.99        13.05        26.01 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        38.04        42.02        14.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F 
       32.02        12.00        31.00        33.04         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 
        2.01        41.00        39.98        40.96        21.37         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        5.79        22.42        27.42         0.20        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        15.75        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25        50.37         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        1.94         2.24         3.06         0.07         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
      102.44        49.08         2.01        20.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        17.75        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        7.50       131.51         7.76         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 
      119.93        35.97        13.38         6.18        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       33.67         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 
       82.39        23.51        74.56        65.85        44.68        45.11 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       39.42        36.00        26.43        35.80        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       47.15        18.18        19.33        15.65        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       42.77        29.46         9.70        30.28        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-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       11.84         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       34.03         0.99        19.99        19.99         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        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         0.99         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         0.49         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 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.99        12.00        36.00        10.98        30.05        13.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06        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        37.51        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-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       43.43        42.90        24.33        37.05        37.25        37.02 
TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       31.63        22.09        22.06         8.38        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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 
       35.01        63.98         1.02        13.02         1.02        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 
        8.05        19.07         0.00        19.07        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       23.01        61.02         6.97        54.02         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.01        11.01        36.00         5.03        26.99        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-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
        0.00        33.07         0.00        36.03        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       18.05        31.00        24.00        33.01        24.00         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A 
        2.01        21.99        34.06        25.02        24.00        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A01P 
       17.03        21.99        34.98        10.98        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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F 
       39.06        51.98         5.03         0.92        22.03        18.05 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
        0.07         4.21        56.55         0.72        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.92        27.09         0.20        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        83.80        61.41         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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.33         0.10        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.99        21.14         2.93       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       25.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64         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        13.64        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6302 
       35.87         1.55        16.31        13.25        19.43        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6321 
       53.62        55.04        51.75        35.93        36.72        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        52.80        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        9.93        12.79        32.98         8.42        31.30        70.03 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72        16.83        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       24.00         2.01        50.04        12.03         6.05        15.95 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 
        7.99         1.02        32.98         0.99         1.02        13.02 
TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       48.03        20.98        13.94        23.01        37.02         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       31.00        10.98        61.97        41.00         1.45         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6681 TCGA-DT-5265 
       10.19         6.05        13.97        15.02        12.95         5.29 
TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 
      126.44         2.40        19.96        20.91         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       17.46         8.45         0.53         1.12         0.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            131.51             140.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             19.00              19.33 
[1] "0.1 - 131.5 (19.0)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   251 110
  13Q GAIN WILD-TYPE 191  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    251  110
  13Q GAIN WILD-TYPE  191   52
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON               251                191
  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        86         4         3
  13Q GAIN WILD-TYPE      44        1       18        85         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED          15         17         53         37       47
  13Q GAIN WILD-TYPE        11          4         26         17       14
                    vv
clus                 STAGE IVA STAGE IVB
  13Q GAIN MUTATED          17         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                86                 85
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                15                 11
  STAGE IIIA               17                  4
  STAGE IIIB               53                 26
  STAGE IIIC               37                 17
  STAGE IV                 47                 14
  STAGE IVA                17                 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  61 249  40
  13Q GAIN WILD-TYPE   6  46 164  26
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                  6
  T2               61                 46
  T3              249                164
  T4               40                 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   181 103  79
  13Q GAIN WILD-TYPE 161  46  35
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0              181                161
  N1              103                 46
  N2               79                 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   261  61
  13Q GAIN WILD-TYPE 187  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    261   61
  13Q GAIN WILD-TYPE  187   25
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              261                187
  1               61                 25
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   165 200
  13Q GAIN WILD-TYPE 121 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    165  200
  13Q GAIN WILD-TYPE  121  122
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE              165                121
  MALE                200                122
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                    234                            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
D25V9, multiclass
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        234                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"
D25V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     7 358
  13Q GAIN WILD-TYPE   2 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7  358
  13Q GAIN WILD-TYPE    2  241
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 7                  2
  YES              358                241
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   255   3  26  12
  13Q GAIN WILD-TYPE 184   2  10  17
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              255                184
  R1                3                  2
  R2               26                 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                          36   189
  13Q GAIN WILD-TYPE                        24   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                      36                 24
  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"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    35   6
  14Q GAIN WILD-TYPE 433 109
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                542 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                109 
$`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         2.24         1.35        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-3999 
       46.75        47.15        12.79        29.46        15.39        28.04 
TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01Y TCGA-EI-6512 TCGA-EI-6885 
       15.95        12.00        64.01        17.69        13.64 

$`14Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        46.65        43.43 
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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        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-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        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-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-3543 
        0.00        19.07        34.03        29.00        29.00         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-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
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-3854 
       14.93         0.00        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-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-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-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-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        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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-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-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21        56.55         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-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        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 
       83.80        22.36        65.00        62.79        61.41        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-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         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 
        0.26         0.33         0.10        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        13.51        11.51 
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-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.17        91.79        52.80        18.18        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        13.05        12.00        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30         9.70        30.28        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-6655 
       12.72        37.74        10.39        14.50        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-3593 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-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        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         1.02        32.98         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-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       14.01         1.02        48.03        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         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         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-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-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        17.46        11.97         8.45         9.96        37.51 
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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             95.18             140.38 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            17.690             19.085 
[1] "0.0 - 95.2 (17.7)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    35   8
  14Q GAIN WILD-TYPE 407 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     35    8
  14Q GAIN WILD-TYPE  407  154
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON                35                407
  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       160        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         20         72         49       57
                    vv
clus                 STAGE IVA STAGE IVB
  14Q GAIN MUTATED           3         1
  14Q GAIN WILD-TYPE        24         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                160
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                1                 20
  STAGE IIIB                7                 72
  STAGE IIIC                5                 49
  STAGE IV                  4                 57
  STAGE IVA                 3                 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
  14Q GAIN MUTATED     1   6  31   5
  14Q GAIN WILD-TYPE  19 101 382  61
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                 19
  T2                6                101
  T3               31                382
  T4                5                 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
  14Q GAIN MUTATED    22  11  10
  14Q GAIN WILD-TYPE 320 138 104
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               22                320
  N1               11                138
  N2               10                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"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    28   8
  14Q GAIN WILD-TYPE 420  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     28    8
  14Q GAIN WILD-TYPE  420   78
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               28                420
  1                8                 78
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    20  23
  14Q GAIN WILD-TYPE 266 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20   23
  14Q GAIN WILD-TYPE  266  299
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               20                266
  MALE                 23                299
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                     26                             9
  14Q GAIN WILD-TYPE                  355                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                       8                              0
  14Q GAIN WILD-TYPE                   138                             13
D26V9, multiclass
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         26                355
  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"
D26V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  42
  14Q GAIN WILD-TYPE   8 557
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   42
  14Q GAIN WILD-TYPE    8  557
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  8
  YES               42                557
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    30   0   1   3
  14Q GAIN WILD-TYPE 409   5  35  26
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               30                409
  R1                0                  5
  R2                1                 35
  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                        58   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                 58
  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"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    11   3
  15Q GAIN WILD-TYPE 457 112
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                569 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                112 
$`15Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-6649 TCGA-AA-3534 TCGA-AA-3941 TCGA-AZ-4614 TCGA-CA-5254 
       11.47        24.16        29.00        24.00         5.65         2.24 
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        12.72        70.03 
TCGA-EI-7004 TCGA-F5-6464 
        8.45         9.96 

$`15Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        11.47        43.76        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-A6-3807 
       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-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-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-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-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-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-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-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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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         4.21        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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        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        75.25        50.37        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        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19         1.94         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-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        13.51        11.51 
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-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-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        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        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        35.41        19.43       107.67 
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-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        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        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30         9.70        30.28        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-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-3593 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-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        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         1.02        32.98         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-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         0.99        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-A01Y 
       36.03         9.07         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         0.49         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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
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-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-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97        37.51        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 
        0.46        18.28        55.76        47.08        26.43 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.24               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.39             140.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            16.385             19.070 
[1] "2.2 - 82.4 (16.4)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 431 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  431  158
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON                11                431
  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       166        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         21         78         53       59
                    vv
clus                 STAGE IVA STAGE IVB
  15Q GAIN MUTATED           3         0
  15Q GAIN WILD-TYPE        24         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                166
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                0                 21
  STAGE IIIB                1                 78
  STAGE IIIC                1                 53
  STAGE IV                  2                 59
  STAGE IVA                 3                 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
  15Q GAIN MUTATED     0   2   8   5
  15Q GAIN WILD-TYPE  20 105 405  61
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                 20
  T2                2                105
  T3                8                405
  T4                5                 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
  15Q GAIN MUTATED     8   3   4
  15Q GAIN WILD-TYPE 334 146 110
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                8                334
  N1                3                146
  N2                4                110
[1] 3 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 437  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  437   82
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               11                437
  1                4                 82
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 275 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  275  318
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                275
  MALE                  4                318
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                     10                             1
  15Q GAIN WILD-TYPE                  371                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                       2                              2
  15Q GAIN WILD-TYPE                   144                             11
D27V9, multiclass
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                371
  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"
D27V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  14
  15Q GAIN WILD-TYPE   8 585
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   14
  15Q GAIN WILD-TYPE    8  585
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 1                  8
  YES               14                585
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    11   0   1   1
  15Q GAIN WILD-TYPE 428   5  35  28
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               11                428
  R1                0                  5
  R2                1                 35
  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                        59   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                 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"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   115  21
  16P GAIN WILD-TYPE 353  94
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               136                447 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 94 
$`16P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        43.43        24.33        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       16.57        37.25        32.45        30.44        29.19        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-3562 TCGA-AA-3673 TCGA-AA-3678 
       13.02        24.00        19.99        19.99        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.02        19.00        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       33.07         0.99        17.03        24.03        27.02        29.98 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       12.99        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G 
       26.01        27.02        34.03        42.02        15.02        12.00 
TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 
       33.04        40.96        22.42        27.42         0.20         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 
       15.75        17.26        18.84         5.13        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
        5.23         1.94         2.24         3.29         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5348 
       49.08        21.99        20.02         8.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6170 
       16.01        17.03        14.04        29.03        14.99        15.02 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6539 
       10.06        19.59        18.25         1.32        15.12        12.49 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 
       13.41        11.38        38.20        13.38         1.55        82.39 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       65.85        44.68        55.04        45.11        39.42        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-2689 
       13.78        46.75        15.65        12.79         9.70        39.48 
TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3726 
       37.74        15.39        20.02        86.63        65.98         7.99 
TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 
       17.03        19.99        36.03         0.99        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 
        9.07        12.00        31.00        38.96        38.04         0.72 
TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 
       10.19         6.97         9.37        78.12        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 
       12.00        10.06        24.13         0.49        17.69        16.31 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       37.51        28.57         0.39         0.76 

$`16P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       42.28        13.94        37.05        37.02        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-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-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-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 
       34.03        29.00         0.99        14.01        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.05        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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        31.07        53.00        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       33.01        26.01        24.00         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        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21        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-6196 TCGA-AY-6197 
        0.92        14.50        27.09        16.31         0.20        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        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        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         2.93         2.01       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        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75        43.27        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        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        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        67.30        53.62        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 
       36.72        36.00        22.09        26.04        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30        30.28        70.03        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        10.39        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-3593 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-3612 TCGA-AG-3727 
        6.05         0.99        15.95        19.99        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         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-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-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 
       26.43         1.81         6.05         6.05         4.73        13.97 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        7.17        10.98        15.02        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        30.05        12.95        13.05         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24       129.27        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-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        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-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.2                0.0 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.44             140.38 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             19.99              19.04 
[1] "0.2 - 102.4 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.3"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   105  40
  16P GAIN WILD-TYPE 337 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    105   40
  16P GAIN WILD-TYPE  337  122
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON               105                337
  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        32         3         0
  16P GAIN WILD-TYPE      86        0       32       139         7         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           7          9         25         18       17
  16P GAIN WILD-TYPE        19         12         54         36       44
                    vv
clus                 STAGE IVA STAGE IVB
  16P GAIN MUTATED           6         1
  16P GAIN WILD-TYPE        21         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                32                139
  STAGE IIB                 3                  7
  STAGE IIC                 0                  3
  STAGE III                 7                 19
  STAGE IIIA                9                 12
  STAGE IIIB               25                 54
  STAGE IIIC               18                 36
  STAGE IV                 17                 44
  STAGE IVA                 6                 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
  16P GAIN MUTATED     5  25  99  16
  16P GAIN WILD-TYPE  15  82 314  50
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 15
  T2               25                 82
  T3               99                314
  T4               16                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16P GAIN MUTATED    64  46  35
  16P GAIN WILD-TYPE 278 103  79
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               64                278
  N1               46                103
  N2               35                 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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    99  24
  16P GAIN WILD-TYPE 349  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     99   24
  16P GAIN WILD-TYPE  349   62
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               99                349
  1               24                 62
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    70  76
  16P GAIN WILD-TYPE 216 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     70   76
  16P GAIN WILD-TYPE  216  246
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               70                216
  MALE                 76                246
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                     99                             6
  16P GAIN WILD-TYPE                  282                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                      40                              0
  16P GAIN WILD-TYPE                   106                             13
D28V9, multiclass
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         99                282
  COLON MUCINOUS ADENOCARCINOMA                 6                 54
  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"
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4 142
  16P GAIN WILD-TYPE   5 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  142
  16P GAIN WILD-TYPE    5  457
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                  5
  YES              142                457
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED   109   0  10   7
  16P GAIN WILD-TYPE 330   5  26  22
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0              109                330
  R1                0                  5
  R2               10                 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"
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                          15    69
  16P GAIN WILD-TYPE                        45   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                      15                 45
  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"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   113  22
  16Q GAIN WILD-TYPE 355  93
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               135                448 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                22                 93 
$`16Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        43.43        24.33        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6140 
       16.57        37.25        32.45        30.44        29.16        24.13 
TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 
       23.87        29.00        26.01        12.99        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 
       24.00        19.99        50.04        47.01        15.02        19.00 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 
       36.95        37.02        14.93        17.03        33.07         0.99 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       17.03        24.03        27.02        12.99        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q 
       34.03        16.08        26.01        27.02        34.03        42.02 
TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 
       15.02        12.00        33.04        40.96        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 
        0.20         0.95        15.75        17.26        18.84         5.13 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 
       62.79        29.56         5.23         1.94         2.24         3.29 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
      102.44        49.08        21.99        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        16.01        17.03        14.04        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-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
       17.13        12.49        10.13        13.41        11.38        38.20 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 
       35.97         8.61        13.38         1.55        82.39        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 TCGA-NH-A6GB 
       55.04        45.11        39.42        26.43        13.78        15.65 
TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
       12.79         9.70        39.48        37.74        10.39        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 
       20.02        86.63        65.98        17.03        19.99        36.03 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
        0.99        15.95        36.03         9.07        12.00        31.00 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5917 
       38.96        38.04         0.72        10.19         9.37        78.12 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG 
       11.01        12.99        12.00        10.06        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
        0.49        17.69        16.31        37.51        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
        0.66         0.69         0.76 

$`16Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       42.28        13.94        37.05        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
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-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-3870 
       36.03        32.05        31.07        31.07        53.00        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01         2.01        21.99        50.99        13.05        34.06 
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-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-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        10.98        32.02        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-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         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        5.79        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        65.00        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
        6.77        12.10       100.01        11.74         3.19         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14         2.93         2.01       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       25.02        26.04        27.02        29.06        22.03        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       17.75        43.27        17.85         4.80        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        6.12        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        95.18        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        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        35.41        19.43       107.67        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-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       51.75        35.93        36.72        36.00        22.09        26.04 
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        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 
       18.18        10.98        19.33        19.33         9.93        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        70.03        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N 
       19.10        12.72        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-3593 TCGA-AG-3594 
       20.05        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-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       25.97        23.01        37.02         1.02        70.03        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-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        0.49         1.45         0.69        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97         4.73        13.97         7.17        10.98 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        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-F5-6571 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        9.96        31.30        32.19         0.53         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.2                0.0 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            102.44             140.38 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.59              19.07 
[1] "0.2 - 102.4 (19.6)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   102  41
  16Q GAIN WILD-TYPE 340 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    102   41
  16Q GAIN WILD-TYPE  340  121
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON               102                340
  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        31         2         0
  16Q GAIN WILD-TYPE      87        0       32       140         8         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           7         10         27         16       16
  16Q GAIN WILD-TYPE        19         11         52         38       45
                    vv
clus                 STAGE IVA STAGE IVB
  16Q GAIN MUTATED           7         1
  16Q GAIN WILD-TYPE        20         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                31                140
  STAGE IIB                 2                  8
  STAGE IIC                 0                  3
  STAGE III                 7                 19
  STAGE IIIA               10                 11
  STAGE IIIB               27                 52
  STAGE IIIC               16                 38
  STAGE IV                 16                 45
  STAGE IVA                 7                 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
  16Q GAIN MUTATED     5  24  99  15
  16Q GAIN WILD-TYPE  15  83 314  51
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                5                 15
  T2               24                 83
  T3               99                314
  T4               15                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16Q GAIN MUTATED    61  48  34
  16Q GAIN WILD-TYPE 281 101  80
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               61                281
  N1               48                101
  N2               34                 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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    97  24
  16Q GAIN WILD-TYPE 351  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     97   24
  16Q GAIN WILD-TYPE  351   62
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               97                351
  1               24                 62
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    69  75
  16Q GAIN WILD-TYPE 217 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     69   75
  16Q GAIN WILD-TYPE  217  247
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               69                217
  MALE                 75                247
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                     96                             6
  16Q GAIN WILD-TYPE                  285                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                      41                              0
  16Q GAIN WILD-TYPE                   105                             13
D29V9, multiclass
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         96                285
  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"
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4 140
  16Q GAIN WILD-TYPE   5 459
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4  140
  16Q GAIN WILD-TYPE    5  459
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                  5
  YES              140                459
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED   109   0   9   6
  16Q GAIN WILD-TYPE 330   5  27  23
D29V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0              109                330
  R1                0                  5
  R2                9                 27
  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                          15    73
  16Q GAIN WILD-TYPE                        45   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                      15                 45
  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"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    36   2
  17P GAIN WILD-TYPE 432 113
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                545 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                113 
$`17P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 
       11.47         4.80        11.47        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       102.44 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6929 
       22.03        14.04        11.01        15.12         4.80        13.41 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QG-A5YW 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 
       13.05        26.43 

$`17P GAIN WILD-TYPE`
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-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        14.53        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05         1.02        35.01        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-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-3818 TCGA-AA-3819 
       26.99        19.04        19.04        10.06         0.99        25.02 
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-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-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-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-3976 TCGA-AA-3977 
       34.03        21.99        16.08        50.99        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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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         4.21        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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        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        75.25        50.37        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        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         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10         1.35        17.56        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         1.32        43.27        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       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-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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        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        13.05        12.00        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30         9.70        30.28        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        12.72 
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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99         0.99         1.02        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-4008 TCGA-AG-4022 
       19.99        28.04        36.03        14.04        17.03         0.99 
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         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00        10.98        30.05        12.95        10.06         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        37.51        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 
        0.76         0.46        18.28        55.76        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            102.44             140.38 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.51              19.07 
[1] "0.1 - 102.4 (18.5)" "0.0 - 140.4 (19.1)"
[1] "hr=" "4"  
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29   9
  17P GAIN WILD-TYPE 413 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29    9
  17P GAIN WILD-TYPE  413  153
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON                29                413
  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       161        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           0          2          5          6        3
  17P GAIN WILD-TYPE        26         19         74         48       58
                    vv
clus                 STAGE IVA STAGE IVB
  17P GAIN MUTATED           3         0
  17P GAIN WILD-TYPE        24         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                161
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                2                 19
  STAGE IIIB                5                 74
  STAGE IIIC                6                 48
  STAGE IV                  3                 58
  STAGE IVA                 3                 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
  17P GAIN MUTATED     3   7  24   4
  17P GAIN WILD-TYPE  17 100 389  62
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                3                 17
  T2                7                100
  T3               24                389
  T4                4                 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
  17P GAIN MUTATED    20  11   7
  17P GAIN WILD-TYPE 322 138 107
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               20                322
  N1               11                138
  N2                7                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"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    25   6
  17P GAIN WILD-TYPE 423  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     25    6
  17P GAIN WILD-TYPE  423   80
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               25                423
  1                6                 80
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    18  20
  17P GAIN WILD-TYPE 268 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18   20
  17P GAIN WILD-TYPE  268  302
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               18                268
  MALE                 20                302
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                     24                             5
  17P GAIN WILD-TYPE                  357                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                       8                              1
  17P GAIN WILD-TYPE                   138                             12
D30V9, multiclass
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         24                357
  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"
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  38
  17P GAIN WILD-TYPE   9 561
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   38
  17P GAIN WILD-TYPE    9  561
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  9
  YES               38                561
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    28   0   2   2
  17P GAIN WILD-TYPE 411   5  34  27
D30V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               28                411
  R1                0                  5
  R2                2                 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"
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                        54   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                 54
  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"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    90  13
  17Q GAIN WILD-TYPE 378 102
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               103                480 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                102 
$`17Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 TCGA-A6-3810 
       11.47        11.47        43.43        24.33        37.02        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 
       14.53        30.44        29.19        29.16        27.09        25.08 
TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 
       25.18        24.69         1.02         1.02        58.03        24.00 
TCGA-AA-3556 TCGA-AA-3692 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 
       23.01        36.00        35.05         1.02        17.03         0.99 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 
       24.03        12.99        34.03         2.01        50.99        13.05 
TCGA-AA-3975 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S TCGA-AD-6888 
       34.06        38.04        21.99        12.00         1.02         4.21 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 
        0.79        27.42        16.44        16.31        61.41        29.56 
TCGA-AZ-6607 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.19         0.07       102.44         8.02        29.06        22.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 
       17.03        14.04        29.03        21.99        14.99        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 
       11.08        11.01        19.59        11.51         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M 
        4.80        17.13        13.41       130.65         6.12        95.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       74.56        65.85        55.04        45.11        39.42        36.00 
TCGA-G4-6626 TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56N 
       46.75        29.46        30.28        17.23        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 
       12.00        46.03        34.03        15.95        19.99        19.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N 
       36.03         1.02        17.03        15.95         9.07        31.00 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 TCGA-DY-A1DG 
        0.69        26.43         6.05        12.00        13.05        51.48 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 
       17.00        18.28        16.31        11.97        32.19         0.46 
TCGA-G5-6641 
       26.43 

$`17Q 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-A6-2680 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-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.25        34.65        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        24.16        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-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-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-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        17.95        29.95        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-3696 
       15.02        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        10.06         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-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-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05        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-3955 TCGA-AA-3968 
       33.01        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       16.08        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-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01        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-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       21.37        56.55         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.20         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        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        75.25        50.37        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        83.80        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         1.94         2.24         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        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        13.51        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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         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        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        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 
       35.41        19.43       107.67        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        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        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        47.15        52.80        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        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.00        42.77        32.98         8.42        31.30         9.70 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        65.98        36.03        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
        7.07        36.03        20.05        24.00         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
       50.04        12.03         6.05         0.99        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         1.02        32.98         0.99         0.99 
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-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         1.02        12.00        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-6644 TCGA-AH-6903 
       41.00        38.04         0.49         1.45         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       20.91        15.85        17.69        16.34        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-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30        28.57         0.39         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            130.65             140.38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            19.990             19.055 
[1] "0.1 - 130.7 (20.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.7"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    78  30
  17Q GAIN WILD-TYPE 364 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     78   30
  17Q GAIN WILD-TYPE  364  132
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON                78                364
  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        28         0         0
  17Q GAIN WILD-TYPE      88        1       33       143        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           3          5         14         12       15
  17Q GAIN WILD-TYPE        23         16         65         42       46
                    vv
clus                 STAGE IVA STAGE IVB
  17Q GAIN MUTATED           8         1
  17Q GAIN WILD-TYPE        19         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                28                143
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                5                 16
  STAGE IIIB               14                 65
  STAGE IIIC               12                 42
  STAGE IV                 15                 46
  STAGE IVA                 8                 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
  17Q GAIN MUTATED     5  19  75   9
  17Q GAIN WILD-TYPE  15  88 338  57
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                 15
  T2               19                 88
  T3               75                338
  T4                9                 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
  17Q GAIN MUTATED    55  29  23
  17Q GAIN WILD-TYPE 287 120  91
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               55                287
  N1               29                120
  N2               23                 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"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    69  23
  17Q GAIN WILD-TYPE 379  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     69   23
  17Q GAIN WILD-TYPE  379   63
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               69                379
  1               23                 63
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    51  57
  17Q GAIN WILD-TYPE 235 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51   57
  17Q GAIN WILD-TYPE  235  265
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               51                235
  MALE                 57                265
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                     69                             8
  17Q GAIN WILD-TYPE                  312                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                      29                              1
  17Q GAIN WILD-TYPE                   117                             12
D31V9, multiclass
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         69                312
  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"
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1 107
  17Q GAIN WILD-TYPE   8 492
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1  107
  17Q GAIN WILD-TYPE    8  492
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 1                  8
  YES              107                492
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    76   1  10   2
  17Q GAIN WILD-TYPE 363   4  26  27
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               76                363
  R1                1                  4
  R2               10                 26
  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                          12    58
  17Q GAIN WILD-TYPE                        48   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                      12                 48
  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"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    23   8
  18P GAIN WILD-TYPE 445 107
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                31                552 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                107 
$`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-AY-6196 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6171 
       37.02         0.07         0.20         3.19        27.02        14.04 
TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 
       13.05        11.08        17.75        16.14        10.13        11.64 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28K TCGA-G4-6299 TCGA-NH-A50V TCGA-NH-A6GA 
        7.50         6.12        98.24        74.56        19.33         9.93 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-A01Y TCGA-AG-A02G TCGA-DT-5265 
       10.39        32.02         6.05        64.01        38.96         5.29 
TCGA-F5-6464 
        9.96 

$`18P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-A6-6654 
       25.08        25.18        20.61        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-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-3666 TCGA-AA-3667 
       61.02        78.08         6.05         6.97         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-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        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-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-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-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-A01F TCGA-AA-A01G 
       21.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       33.04        35.01        26.01        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         4.21        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        15.75        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        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        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         1.94         2.24 
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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04         8.02        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        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        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        13.51        11.51        20.19 
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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        13.41         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-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        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        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        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        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       52.80        18.18        10.98        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30         9.70        30.28        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        12.72        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-3593 
       36.03        20.05        24.00         1.02        46.03        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-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       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-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-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45        37.51        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         0.46        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             140.38 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             11.64              19.38 
[1] "0.1 - 98.2 (11.6)"  "0.0 - 140.4 (19.4)"
[1] "hr=" "1.5"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25   8
  18P GAIN WILD-TYPE 417 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25    8
  18P GAIN WILD-TYPE  417  154
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON                25                417
  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       167        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         20         76         47       57
                    vv
clus                 STAGE IVA STAGE IVB
  18P GAIN MUTATED           0         1
  18P GAIN WILD-TYPE        27         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                167
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                1                 20
  STAGE IIIB                3                 76
  STAGE IIIC                7                 47
  STAGE IV                  4                 57
  STAGE IVA                 0                 27
  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  20 101 391  61
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                 20
  T2                6                101
  T3               22                391
  T4                5                 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
  18P GAIN MUTATED    14   6  13
  18P GAIN WILD-TYPE 328 143 101
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               14                328
  N1                6                143
  N2               13                101
[1] 3 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 424  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24    4
  18P GAIN WILD-TYPE  424   82
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               24                424
  1                4                 82
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    11  22
  18P GAIN WILD-TYPE 275 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11   22
  18P GAIN WILD-TYPE  275  300
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                275
  MALE                 22                300
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                     18                             7
  18P GAIN WILD-TYPE                  363                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                       6                              2
  18P GAIN WILD-TYPE                   140                             11
D32V9, multiclass
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         18                363
  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"
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  32
  18P GAIN WILD-TYPE   8 567
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   32
  18P GAIN WILD-TYPE    8  567
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  8
  YES               32                567
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    23   0   1   1
  18P GAIN WILD-TYPE 416   5  35  28
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               23                416
  R1                0                  5
  R2                1                 35
  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                        57   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                 57
  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"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    14   3
  18Q GAIN WILD-TYPE 454 112
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                17                566 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                112 
$`18Q GAIN MUTATED`
TCGA-A6-6653 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AD-5900 TCGA-AY-6196 
       24.39        54.02         5.98        10.06         0.07         0.20 
TCGA-AZ-6607 TCGA-CM-6171 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 
        3.19        14.04        17.75        16.14        10.13        11.64 
TCGA-DM-A28K TCGA-G4-6299 TCGA-AF-6672 TCGA-DT-5265 TCGA-F5-6464 
       98.24        74.56        10.39         5.29         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-A6-6654 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-3666 
       19.99        61.02        78.08         6.05         6.97         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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        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-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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        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        15.75 
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 
       75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
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         1.94         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
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-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        13.41         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-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-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05        12.00 
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         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        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        12.72        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-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-3593 TCGA-AG-3594 
       20.05        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-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       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-F5-6465 
       10.78        13.64        17.46        11.97         8.45        37.51 
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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.24             140.38 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.39              19.33 
[1] "0.1 - 98.2 (10.4)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    15   4
  18Q GAIN WILD-TYPE 427 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     15    4
  18Q GAIN WILD-TYPE  427  158
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON                15                427
  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       168        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         20         79         51       59
                    vv
clus                 STAGE IVA STAGE IVB
  18Q GAIN MUTATED           0         0
  18Q GAIN WILD-TYPE        27         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                168
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                1                 20
  STAGE IIIB                0                 79
  STAGE IIIC                3                 51
  STAGE IV                  2                 59
  STAGE IVA                 0                 27
  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  20 103 402  62
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                 20
  T2                4                103
  T3               11                402
  T4                4                 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
  18Q GAIN MUTATED    10   3   6
  18Q GAIN WILD-TYPE 332 146 108
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               10                332
  N1                3                146
  N2                6                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"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    14   1
  18Q GAIN WILD-TYPE 434  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     14    1
  18Q GAIN WILD-TYPE  434   85
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               14                434
  1                1                 85
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  13
  18Q GAIN WILD-TYPE 280 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   13
  18Q GAIN WILD-TYPE  280  309
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                280
  MALE                 13                309
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                     10                             5
  18Q GAIN WILD-TYPE                  371                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                       3                              1
  18Q GAIN WILD-TYPE                   143                             12
D33V9, multiclass
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                371
  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"
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  18
  18Q GAIN WILD-TYPE   8 581
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   18
  18Q GAIN WILD-TYPE    8  581
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                  8
  YES               18                581
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    13   0   0   1
  18Q GAIN WILD-TYPE 426   5  36  28
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               13                426
  R1                0                  5
  R2                0                 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"
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                        60   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                 60
  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"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    80  17
  19P GAIN WILD-TYPE 388  98
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                97                486 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                17                 98 
$`19P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
       11.47        11.47        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        61.41        29.56        11.74         3.06 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 
        1.35        40.34        21.99         2.01        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 
       29.06        16.01         5.03        15.02        15.02        14.04 
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        13.51 
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        45.11        39.42        26.43        47.15        13.05 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L 
       29.46         9.70        39.48        17.23        86.63        65.98 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 
       36.03        46.03         6.05        19.99         0.99        19.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N 
        1.02        36.03         1.02        15.95        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 
        1.94        38.04         6.05        10.98        11.01        12.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 
       36.00        13.05       129.27        20.55        17.69        16.31 
TCGA-F5-6863 
        0.76 

$`19P GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        4.80        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        13.94        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        20.61        24.69        24.39 
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-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-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-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-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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        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-3975 TCGA-AA-3976 
       34.03         2.01        21.99        16.08        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07         7.96        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-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-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-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-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        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         4.21        56.55         0.79         0.72 
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-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        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        75.25        50.37 
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        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
      100.01         5.23         3.19         1.94         2.24         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         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        70.16        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        27.02        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        17.03        12.00        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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-G4-6321 TCGA-G4-6322 
       51.75        35.93        36.72        36.00        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        12.00        42.77        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        70.03        24.13        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        8.02         7.07        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-3612 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
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-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         9.07         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.97        38.96        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       78.12         7.17        15.02        12.99        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        30.05        12.95        10.06         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-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        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-F5-6571 
       17.46        11.97         8.45         9.96        37.51        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         0.46        18.28        55.76        47.08        26.43 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.76               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             140.38 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             19.99              19.04 
[1] "0.8 - 129.3 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    72  32
  19P GAIN WILD-TYPE 370 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     72   32
  19P GAIN WILD-TYPE  370  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON                72                370
  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       140        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           4          3         18          7       12
  19P GAIN WILD-TYPE        22         18         61         47       49
                    vv
clus                 STAGE IVA STAGE IVB
  19P GAIN MUTATED           5         0
  19P GAIN WILD-TYPE        22         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                140
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 4                 22
  STAGE IIIA                3                 18
  STAGE IIIB               18                 61
  STAGE IIIC                7                 47
  STAGE IV                 12                 49
  STAGE IVA                 5                 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
  19P GAIN MUTATED     2  18  74  10
  19P GAIN WILD-TYPE  18  89 339  56
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                2                 18
  T2               18                 89
  T3               74                339
  T4               10                 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
  19P GAIN MUTATED    57  31  16
  19P GAIN WILD-TYPE 285 118  98
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               57                285
  N1               31                118
  N2               16                 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"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    70  17
  19P GAIN WILD-TYPE 378  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     70   17
  19P GAIN WILD-TYPE  378   69
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               70                378
  1               17                 69
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    44  60
  19P GAIN WILD-TYPE 242 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     44   60
  19P GAIN WILD-TYPE  242  262
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               44                242
  MALE                 60                262
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                     65                             7
  19P GAIN WILD-TYPE                  316                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                      32                              0
  19P GAIN WILD-TYPE                   114                             13
D34V9, multiclass
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         65                316
  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"
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1 103
  19P GAIN WILD-TYPE   8 496
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1  103
  19P GAIN WILD-TYPE    8  496
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                  8
  YES              103                496
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    75   2   5   7
  19P GAIN WILD-TYPE 364   3  31  22
D34V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               75                364
  R1                2                  3
  R2                5                 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"
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                        45   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                 45
  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"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    88  18
  19Q GAIN WILD-TYPE 380  97
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               106                477 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                 97 
$`19Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
       11.47        11.47        43.76        43.43        45.60        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 
       37.02        36.53        14.53        31.63        29.16        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 
       25.18        21.76        23.87        61.84        56.25        35.01 
TCGA-AA-3506 TCGA-AA-3529 TCGA-AA-3542 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3854 
       58.03         0.00        12.99        35.05         0.99        36.03 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q 
       12.99        50.99        13.05        18.05        27.02        42.02 
TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       12.00        51.98         0.92         5.79        22.42        16.44 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
        0.20        17.85        18.84        61.41        29.56        11.74 
TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
        3.06         1.35        40.34        21.99         2.01        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        16.01         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 
       15.02        14.04        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        13.64        35.41        82.39        45.11 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QL-A97D 
       39.42        26.43        47.15        13.05        29.46         9.70 
TCGA-AF-2689 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3878 
       39.48        86.63        65.98        46.03        19.99         0.99 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       19.99         1.02         1.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CL-4957 
       12.00        31.00         1.94        38.04         6.05        13.97 
TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 
       11.01        12.00        36.00        13.05       129.27        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       17.69        16.31        13.64         0.76 

$`19Q GAIN WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        4.80        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        13.94        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 
       19.66        20.28        16.24        24.92         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 
        7.04         3.02         1.02        37.05         1.02        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-3530 
       24.03        37.05        36.03         8.05        19.07        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-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-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-3819 TCGA-AA-3821 
       26.99        19.04        19.04        10.06        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-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-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-3975 TCGA-AA-3976 
       34.03         2.01        21.99        16.08        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-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04         4.01         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-A01I 
       34.98        15.02        15.02        10.98        32.02        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-A02E TCGA-AA-A02F 
       35.01        26.01        37.02        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        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         4.21        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-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.26        19.33        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
        5.23         3.19         1.94         2.24         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         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        70.16        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 
        2.93       124.27        23.05        20.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 
       27.02        22.03        22.98        30.08        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       17.03        12.00        16.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        9.44        13.41         1.51        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-A28G 
        6.12        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24        95.18        13.38        11.11        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        19.43       107.67        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-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        35.93        36.72        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        52.80        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        12.00        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
        8.42        31.30        30.28        70.03        24.13        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        12.72        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-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 
        0.99        29.98         1.02        32.98         0.99         1.02 
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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       37.02         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        41.00         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        0.69         0.72        26.43         1.81        10.19         6.05 
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        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        13.97        15.02        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       24.13        51.48        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        18.28        15.85        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-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             140.38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            19.215             19.070 
[1] "0.0 - 129.3 (19.2)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    81  32
  19Q GAIN WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     81   32
  19Q GAIN WILD-TYPE  361  130
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON                81                361
  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        32         0         0
  19Q GAIN WILD-TYPE      83        1       32       139        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           3          4         18          9       14
  19Q GAIN WILD-TYPE        23         17         61         45       47
                    vv
clus                 STAGE IVA STAGE IVB
  19Q GAIN MUTATED           6         0
  19Q GAIN WILD-TYPE        21         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                32                139
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 3                 23
  STAGE IIIA                4                 17
  STAGE IIIB               18                 61
  STAGE IIIC                9                 45
  STAGE IV                 14                 47
  STAGE IVA                 6                 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
  19Q GAIN MUTATED     3  21  77  12
  19Q GAIN WILD-TYPE  17  86 336  54
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 17
  T2               21                 86
  T3               77                336
  T4               12                 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
  19Q GAIN MUTATED    61  34  18
  19Q GAIN WILD-TYPE 281 115  96
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               61                281
  N1               34                115
  N2               18                 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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    74  20
  19Q GAIN WILD-TYPE 374  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     74   20
  19Q GAIN WILD-TYPE  374   66
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               74                374
  1               20                 66
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    50  63
  19Q GAIN WILD-TYPE 236 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     50   63
  19Q GAIN WILD-TYPE  236  259
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               50                236
  MALE                 63                259
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                     70                            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
D35V9, multiclass
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         70                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"
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1 112
  19Q GAIN WILD-TYPE   8 487
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1  112
  19Q GAIN WILD-TYPE    8  487
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  8
  YES              112                487
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    80   2   6   7
  19Q GAIN WILD-TYPE 359   3  30  22
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               80                359
  R1                2                  3
  R2                6                 30
  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                          17    59
  19Q GAIN WILD-TYPE                        43   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                      17                 43
  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"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   267  68
  20P GAIN WILD-TYPE 201  47
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               335                248 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                68                 47 
$`20P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       30.44        29.19        23.61        27.09        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       24.16        21.76        24.69        23.87        20.28        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 
       58.03         6.97         1.02        36.03         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 
       34.03        29.00        29.00        12.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 
       13.02        23.01        20.98        13.94        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.05        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        0.99        25.02        38.99        37.02        14.93         0.00 
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-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       17.03        27.02        18.05        12.99        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K 
       24.00        27.02        19.07         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C 
       38.04         4.01        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01T 
       10.98        32.02        12.00        31.00        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       41.00        39.98         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
        0.72         5.79        22.42        27.42        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
       14.50        16.31         0.95        15.75        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
       19.33        18.84         1.41         5.13        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        49.41        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-4744 
        1.35        17.56       102.44        40.34        49.08        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 
       25.02         8.02        13.02        29.06        22.98         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       21.99        14.99        13.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       11.08        11.01        45.40        12.26        19.59        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.75         1.32        17.85        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       10.13         9.04        11.64        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F 
        7.50       139.17         6.12        14.04       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        95.18         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 
        1.55        29.59        33.67        35.41       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       82.39        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15        18.18 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        12.00        42.77        29.46        32.98 
TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 
        9.70        24.13        39.48        17.23        19.10        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3580 
       10.39        16.83        20.02        10.39        65.98         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-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       34.03        50.04        12.03        15.95        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99        29.98         1.02         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       36.95        17.03        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-A00C 
       28.04        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 
       25.97        23.01        37.02        36.03         9.07        51.98 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        4.73        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
       12.95       126.44        41.36       129.27        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       17.69        16.31        11.51        10.78        13.64        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
        9.96        37.51         0.39        32.19         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        18.28        55.76        47.08 

$`20P GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
       11.47        46.65        42.90        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.13         8.38        20.61        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92        56.25         3.02        35.01        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-3526 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 
        8.05        19.07        26.01         0.99        33.99        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       17.95        29.95        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
       54.02         0.92        47.01        11.01         5.98        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
       19.04        19.04         1.02        17.98        15.95        36.95 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3867 
        0.00         0.00        36.03        32.05        53.00        24.03 
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-3966 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
        2.01         2.01        34.06        25.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        34.98        15.02        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R 
        1.02        35.01        37.02        39.06        39.98        22.03 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
       18.05        40.96        56.55        10.88         0.20         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 
       27.09         0.20        21.44        17.82        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        22.36        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
      100.01        11.74         3.25         0.26         0.33         0.10 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
        2.01       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 
       22.03        30.08        16.01        15.02        12.00        29.03 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 
       12.99        15.02        12.95        13.05        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.42        18.25        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 
        4.80        17.13        16.14        15.58        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 
        9.44         1.51        12.00        92.75        49.91       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C 
       44.32       131.51       135.65         7.76        26.47        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 
       60.79        98.24        11.11        13.64        35.87        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6298 
       16.24        13.25         0.53        19.43         8.35        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        51.75 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       36.00        26.43        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5Z1 
       10.98        19.33        19.33         9.93        13.05         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       31.30        30.28        70.03        43.04        13.55        12.72 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3732 
       32.02         2.01         6.05         0.99         7.99        32.98 
TCGA-AG-3882 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A002 
       19.99        13.02        35.01        32.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       13.94        15.95         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.05        78.12         7.17        13.05        10.06         5.29 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6881 
       57.24        51.48         0.49        19.96        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 
        8.61        17.46         8.45        31.30        28.57         0.69 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        26.43 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            139.17             140.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             17.56              21.29 
[1] "0.0 - 139.2 (17.6)" "0.0 - 140.4 (21.3)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   241 106
  20P GAIN WILD-TYPE 201  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    241  106
  20P GAIN WILD-TYPE  201   56
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON               241                201
  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        86         4         2
  20P GAIN WILD-TYPE      41        0       23        85         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          13         18         41         32       47
  20P GAIN WILD-TYPE        13          3         38         22       14
                    vv
clus                 STAGE IVA STAGE IVB
  20P GAIN MUTATED          18         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                86                 85
  STAGE IIB                 4                  6
  STAGE IIC                 2                  1
  STAGE III                13                 13
  STAGE IIIA               18                  3
  STAGE IIIB               41                 38
  STAGE IIIC               32                 22
  STAGE IV                 47                 14
  STAGE IVA                18                  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  67 233  35
  20P GAIN WILD-TYPE   8  40 180  31
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               12                  8
  T2               67                 40
  T3              233                180
  T4               35                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20P GAIN MUTATED   181  91  74
  20P GAIN WILD-TYPE 161  58  40
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              181                161
  N1               91                 58
  N2               74                 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"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   246  64
  20P GAIN WILD-TYPE 202  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    246   64
  20P GAIN WILD-TYPE  202   22
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              246                202
  1               64                 22
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   156 193
  20P GAIN WILD-TYPE 130 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    156  193
  20P GAIN WILD-TYPE  130  129
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              156                130
  MALE                193                129
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                    220                            20
  20P GAIN WILD-TYPE                  161                            40
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                     100                              4
  20P GAIN WILD-TYPE                    46                              9
D36V9, multiclass
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        220                161
  COLON MUCINOUS ADENOCARCINOMA                20                 40
  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"
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 342
  20P GAIN WILD-TYPE   2 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  342
  20P GAIN WILD-TYPE    2  257
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                  2
  YES              342                257
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   247   3  25  11
  20P GAIN WILD-TYPE 192   2  11  18
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              247                192
  R1                3                  2
  R2               25                 11
  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                          33   172
  20P GAIN WILD-TYPE                        27   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                      33                 27
  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"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   356  84
  20Q GAIN WILD-TYPE 112  31
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               440                143 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                84                 31 
$`20Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 
       58.03         6.97         1.02        38.99         9.07        36.03 
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-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.05         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 
       85.05        10.06        35.05         0.99        25.02        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-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       33.07        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       24.03        27.02        18.05        12.99        24.00        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-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       13.94        19.00        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
        1.02        33.04        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42         0.20        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L 
       14.50        16.31         0.95        15.75         0.20        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 
       17.85        19.33        18.84        75.25         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
      102.44        40.34        49.08        21.99         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       14.99        13.02        15.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        17.75        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       13.25         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       82.39        23.51        74.56        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15        18.18 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42         9.70        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
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-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        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-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        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-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        41.00        38.04         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37         4.73        13.97         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
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-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         9.96        37.51 
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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`20Q GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
       11.47        46.65        42.90        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        61.02         6.97        54.02         0.92 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 
       11.01         5.98        26.99        19.04        19.04         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
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-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        2.01        25.02        27.02        38.04        30.02        18.05 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
        0.99        34.98        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 
       39.06        22.03        18.05        56.55        10.88         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       27.09        21.44        17.82        50.37        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 
       32.94        61.41         6.77       100.01        11.74         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.33         0.10        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
        2.93       124.27        23.05        26.04        27.02        15.02 
TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 
       12.00        12.99        12.95        13.05        12.03        20.42 
TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       43.27        16.14        15.58         9.44         1.51        12.00 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
       92.75       140.38       131.51       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        35.87        19.43        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       53.62        51.75        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       10.98        19.33        19.33         9.93        31.30        70.03 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        12.72        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CL-5917 
       32.98        13.02        20.98        49.97        61.97        78.12 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        5.29        19.96         8.61        17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            139.17             140.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             18.05              21.44 
[1] "0.0 - 139.2 (18.1)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1.1"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   312 144
  20Q GAIN WILD-TYPE 130  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    312  144
  20Q GAIN WILD-TYPE  130   18
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON               312                130
  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       115         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          18         20         62         44       55
  20Q GAIN WILD-TYPE         8          1         17         10        6
                    vv
clus                 STAGE IVA STAGE IVB
  20Q GAIN MUTATED          24         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               115                 56
  STAGE IIB                 5                  5
  STAGE IIC                 3                  0
  STAGE III                18                  8
  STAGE IIIA               20                  1
  STAGE IIIB               62                 17
  STAGE IIIC               44                 10
  STAGE IV                 55                  6
  STAGE IVA                24                  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  86 312  45
  20Q GAIN WILD-TYPE   6  21 101  21
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               14                  6
  T2               86                 21
  T3              312                101
  T4               45                 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"
                    vv
clus                  N0  N1  N2
  20Q GAIN MUTATED   238 127  91
  20Q GAIN WILD-TYPE 104  22  23
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              238                104
  N1              127                 22
  N2               91                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   327  77
  20Q GAIN WILD-TYPE 121   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    327   77
  20Q GAIN WILD-TYPE  121    9
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              327                121
  1               77                  9
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   210 249
  20Q GAIN WILD-TYPE  76  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    210  249
  20Q GAIN WILD-TYPE   76   73
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              210                 76
  MALE                249                 73
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                    286                            25
  20Q GAIN WILD-TYPE                   95                            35
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                     135                              7
  20Q GAIN WILD-TYPE                    11                              6
D37V9, multiclass
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        286                 95
  COLON MUCINOUS ADENOCARCINOMA                25                 35
  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"
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 451
  20Q GAIN WILD-TYPE   1 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  451
  20Q GAIN WILD-TYPE    1  148
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                  1
  YES              451                148
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   330   4  32  16
  20Q GAIN WILD-TYPE 109   1   4  13
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              330                109
  R1                4                  1
  R2               32                  4
  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                          42   227
  20Q GAIN WILD-TYPE                        18    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                      42                 18
  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"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    24   6
  21Q GAIN WILD-TYPE 444 109
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                30                553 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                109 
$`21Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-5662 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
       11.47        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        61.41         1.94         3.06        17.03        19.59 
TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M 
        7.53        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-3612 
       82.39        19.33        29.46         9.70        30.28        19.99 
TCGA-AG-3732 TCGA-AG-A011 TCGA-AH-6644 TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
       32.98        37.02         0.72         9.37         0.49        13.64 

$`21Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        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-A6-3807 
       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-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        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-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-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-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-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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 
        4.21        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-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        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 
       83.80        22.36        65.00        62.79        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-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
       35.41        19.43       107.67        28.21         8.35        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 
       51.75        45.11        39.42        35.93        36.72        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        47.15        52.80        18.18        10.98 
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        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       42.77        32.98         8.42        31.30        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        12.72 
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-3593 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-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02         0.99         0.99        19.99         1.02 
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         0.99        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-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-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        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-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-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             95.18             140.38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             18.18              19.07 
[1] "0.5 - 95.2 (18.2)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1"  
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    23  10
  21Q GAIN WILD-TYPE 419 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     23   10
  21Q GAIN WILD-TYPE  419  152
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON                23                419
  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       165         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         19         74         52       57
                    vv
clus                 STAGE IVA STAGE IVB
  21Q GAIN MUTATED           2         0
  21Q GAIN WILD-TYPE        25         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                165
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                2                 19
  STAGE IIIB                5                 74
  STAGE IIIC                2                 52
  STAGE IV                  4                 57
  STAGE IVA                 2                 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
  21Q GAIN MUTATED     3   7  22   2
  21Q GAIN WILD-TYPE  17 100 391  64
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 17
  T2                7                100
  T3               22                391
  T4                2                 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
  21Q GAIN MUTATED    16   9   8
  21Q GAIN WILD-TYPE 326 140 106
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               16                326
  N1                9                140
  N2                8                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"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21   6
  21Q GAIN WILD-TYPE 427  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21    6
  21Q GAIN WILD-TYPE  427   80
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               21                427
  1                6                 80
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18  16
  21Q GAIN WILD-TYPE 268 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18   16
  21Q GAIN WILD-TYPE  268  306
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               18                268
  MALE                 16                306
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                     18                             5
  21Q GAIN WILD-TYPE                  363                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                      10                              0
  21Q GAIN WILD-TYPE                   136                             13
D38V9, multiclass
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         18                363
  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"
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  34
  21Q GAIN WILD-TYPE   9 565
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   34
  21Q GAIN WILD-TYPE    9  565
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  9
  YES               34                565
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    21   0   1   2
  21Q GAIN WILD-TYPE 418   5  35  27
D38V11, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               21                418
  R1                0                  5
  R2                1                 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"
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                        55   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                 55
  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"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    18   5
  22Q GAIN WILD-TYPE 450 110
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                560 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                110 
$`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       102.44        14.04        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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       29.16        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-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        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-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-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-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-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-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-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        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        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-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        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         1.94         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
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-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        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 
       13.51        11.51        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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-G4-6315 
       44.68        55.04        51.75        45.11        39.42        36.72 
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        47.15        52.80        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 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       31.30         9.70        70.03        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        12.72        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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        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-3726 
       50.04        12.03         6.05         0.99        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        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         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        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-6903 TCGA-BM-6198 
        0.49         1.45         0.69         0.72         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         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-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        37.51 
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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            102.44             140.38 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 19 
[1] "1.0 - 102.4 (24.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 429 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   10
  22Q GAIN WILD-TYPE  429  152
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON                13                429
  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       168        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0          1          4          4        4
  22Q GAIN WILD-TYPE        26         20         75         50       57
                    vv
clus                 STAGE IVA STAGE IVB
  22Q GAIN MUTATED           1         0
  22Q GAIN WILD-TYPE        26         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                168
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 0                 26
  STAGE IIIA                1                 20
  STAGE IIIB                4                 75
  STAGE IIIC                4                 50
  STAGE IV                  4                 57
  STAGE IVA                 1                 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
  22Q GAIN MUTATED     2   3  18   0
  22Q GAIN WILD-TYPE  18 104 395  66
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                2                 18
  T2                3                104
  T3               18                395
  T4                0                 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
  22Q GAIN MUTATED    10   6   7
  22Q GAIN WILD-TYPE 332 143 107
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               10                332
  N1                6                143
  N2                7                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"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    17   5
  22Q GAIN WILD-TYPE 431  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     17    5
  22Q GAIN WILD-TYPE  431   81
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               17                431
  1                5                 81
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10  13
  22Q GAIN WILD-TYPE 276 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10   13
  22Q GAIN WILD-TYPE  276  309
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               10                276
  MALE                 13                309
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                     13                             0
  22Q GAIN WILD-TYPE                  368                            60
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                      10                              0
  22Q GAIN WILD-TYPE                   136                             13
D39V9, multiclass
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         13                368
  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"
D39V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  22
  22Q GAIN WILD-TYPE   8 577
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   22
  22Q GAIN WILD-TYPE    8  577
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                  8
  YES               22                577
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    16   0   3   0
  22Q GAIN WILD-TYPE 423   5  33  29
D39V11, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               16                423
  R1                0                  5
  R2                3                 33
  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                        59   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                 59
  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"

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    78  16
  XP GAIN WILD-TYPE 390  99
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               94               489 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               16                99 
$`XP GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-6142 TCGA-A6-6650 
       11.47        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         4.21 
TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4682 
       16.44        15.75         0.20        17.26        18.84        22.36 
TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5860 
       49.41         1.94         1.35        21.99         2.01        16.01 
TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-5541 
        5.03        15.02        21.99        14.99        19.59        11.51 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-DM-A0X9 TCGA-DM-A1DA 
       15.12         4.80        17.13        12.49       119.70         7.50 
TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-G4-6299 TCGA-G4-6306 
       35.97        98.24        95.18         8.61        74.56        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-3913 
       55.04        45.11        39.42         9.70        13.55        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 
       16.83        20.02        86.63        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         0.99        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        10.98 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1H8 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
       12.00        15.02        32.61        18.28        17.69        13.64 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6235 
       37.51         0.39         0.76        55.76 

$`XP GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.90        24.33        42.28        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-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-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-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 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-3556 TCGA-AA-3560 
       21.01        13.02        17.95        29.95        23.01        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-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        50.04        47.05        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00        85.05        26.99        19.04 
TCGA-AA-3715 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-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-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-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        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        15.02        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-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-A02F 
       35.01        26.01        37.02        39.06         2.96        39.98 
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-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.95        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
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-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         2.24         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         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       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-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       12.00        14.04        29.03        16.04        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-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       43.27        17.85        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        6.12        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
      117.07        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        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        35.41        19.43       107.67        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-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        35.93        36.72        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 
       47.15        52.80        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        13.05        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       29.46        32.98         8.42        31.30        30.28        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N 
       37.74        14.50        15.39        10.39        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-3593 TCGA-AG-3594 
       20.05        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-3726 
       50.04        12.03         6.05         0.99        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        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-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       37.02         1.02        12.00        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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69        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         6.05         6.97         4.73        13.97         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.99        13.97        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       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-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        17.00        15.85 
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-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19         0.66         0.69         0.53         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           119.70            140.38 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            18.56             19.07 
[1] "0.0 - 119.7 (18.6)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    66  31
  XP GAIN WILD-TYPE 376 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     66   31
  XP GAIN WILD-TYPE  376  131
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON               66               376
  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       151         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         16         59         46       52
                   vv
clus                STAGE IVA STAGE IVB
  XP GAIN MUTATED           9         0
  XP GAIN WILD-TYPE        18         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               151
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                3                23
  STAGE IIIA               5                16
  STAGE IIIB              20                59
  STAGE IIIC               8                46
  STAGE IV                 9                52
  STAGE IVA                9                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
  XP GAIN MUTATED     2  20  70   6
  XP GAIN WILD-TYPE  18  87 343  60
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               2                18
  T2              20                87
  T3              70               343
  T4               6                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
  XP GAIN MUTATED    48  31  17
  XP GAIN WILD-TYPE 294 118  97
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              48               294
  N1              31               118
  N2              17                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"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    67  17
  XP GAIN WILD-TYPE 381  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     67   17
  XP GAIN WILD-TYPE  381   69
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              67               381
  1              17                69
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    53  45
  XP GAIN WILD-TYPE 233 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     53   45
  XP GAIN WILD-TYPE  233  277
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              53               233
  MALE                45               277
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                     58                             8
  XP GAIN WILD-TYPE                  323                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                      31                              0
  XP GAIN WILD-TYPE                   115                             13
D40V9, multiclass
                                clus
vv                               XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        58               323
  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"
D40V10, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  97
  XP GAIN WILD-TYPE   8 502
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   97
  XP GAIN WILD-TYPE    8  502
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                1                 8
  YES              97               502
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    68   1   8   5
  XP GAIN WILD-TYPE 371   4  28  24
D40V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              68               371
  R1               1                 4
  R2               8                28
  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                        48   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                48
  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"

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    79  22
  XQ GAIN WILD-TYPE 389  93
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              101               482 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22                93 
$`XQ GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-6142 TCGA-A6-6650 
       11.47        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-6196 TCGA-AY-A54L 
        0.92        39.98         4.21        16.44         0.20        17.26 
TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6608 
       18.84         5.65        22.36        49.41       100.01         1.94 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 
        1.35        21.99        22.98        16.01         5.03        15.02 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 
       21.99        14.99        13.05        19.59        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A285 
       17.13        12.49        12.43       119.70         7.50         6.12 
TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6299 
       35.97        98.24        95.18         8.61         6.18        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-NH-A6GB TCGA-QL-A97D 
       44.68        55.04        45.11        39.42        15.65         9.70 
TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       70.03        13.55        10.39        16.83        20.02        86.63 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       19.99        19.99        35.01        28.04         1.02         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 
       15.95        36.03         9.07        38.04         0.72         9.37 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-EI-6510 TCGA-EI-6512 
       78.12        10.98        12.00        15.02        18.28        17.69 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       13.64         9.96        37.51         0.39         0.76 

$`XQ GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        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-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        21.76        24.39 
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-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-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-3560 TCGA-AA-3561 
       13.02        17.95        29.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 
       19.99        61.02         6.05         6.97         2.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.05        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 
       36.00        85.05        26.99        19.04        19.04        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-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-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
        7.96        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-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        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        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-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-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       15.75        21.44        17.82        17.85        19.33        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19         2.24         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         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       13.02        29.06        22.03        30.08        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-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        13.51        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 
       18.25         1.32        43.27        17.85        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
      117.07        13.38        11.11        13.64        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       82.39        23.51        67.30        65.85        53.62        51.75 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        8.42        31.30        30.28        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       43.04        19.10        12.72        37.74        14.50        15.39 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95         7.99         0.99        29.98         1.02 
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-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-A002 TCGA-AG-A008 
       19.99        36.03        14.04        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
        6.02        25.97        23.01        37.02         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-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        41.00         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        13.97         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         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-6511 TCGA-EI-6513 
       20.55        19.96        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           119.70            140.38 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           18.280            19.085 
[1] "0.0 - 119.7 (18.3)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1"  
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76  30
  XQ GAIN WILD-TYPE 366 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76   30
  XQ GAIN WILD-TYPE  366  132
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON               76               366
  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       147         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         17         59         44       54
                   vv
clus                STAGE IVA STAGE IVB
  XQ GAIN MUTATED           9         1
  XQ GAIN WILD-TYPE        18         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               147
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               4                17
  STAGE IIIB              20                59
  STAGE IIIC              10                44
  STAGE IV                 7                54
  STAGE IVA                9                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
  XQ GAIN MUTATED     2  19  78   8
  XQ GAIN WILD-TYPE  18  88 335  58
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                18
  T2              19                88
  T3              78               335
  T4               8                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
  XQ GAIN MUTATED    53  30  22
  XQ GAIN WILD-TYPE 289 119  92
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              53               289
  N1              30               119
  N2              22                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"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76  16
  XQ GAIN WILD-TYPE 372  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76   16
  XQ GAIN WILD-TYPE  372   70
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              76               372
  1              16                70
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    57  50
  XQ GAIN WILD-TYPE 229 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     57   50
  XQ GAIN WILD-TYPE  229  272
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              57               229
  MALE                50               272
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                     68                             8
  XQ GAIN WILD-TYPE                  313                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                      29                              0
  XQ GAIN WILD-TYPE                   117                             13
D41V9, multiclass
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        68               313
  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"
D41V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1 106
  XQ GAIN WILD-TYPE   8 493
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1  106
  XQ GAIN WILD-TYPE    8  493
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                1                 8
  YES             106               493
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    79   0   6   5
  XQ GAIN WILD-TYPE 360   5  30  24
D41V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              79               360
  R1               0                 5
  R2               6                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"
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                        46   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                46
  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"

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    99  30
  1P LOSS WILD-TYPE 369  85
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              129               454 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30                85 
$`1P LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
        4.80        43.76        35.11        36.53        14.53        32.45 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3488 TCGA-AA-3517 
       29.19        23.61        22.52        21.76         5.03        38.99 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 
        9.07        37.05        19.99        50.04        37.05        10.06 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3860 TCGA-AA-3866 
       38.99        37.02        10.06        33.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A00F 
       24.03        12.99         2.01        21.99         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       42.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
        2.01        41.00         0.79         5.79        22.42         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 
       16.44        14.50        16.31         5.65         5.13        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CK-6748 
       29.56         5.23         3.19         2.24         2.14         2.01 
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-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6929 
       11.08        10.06        13.51        17.75         1.32        13.41 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-DM-A28A TCGA-F4-6460 
       11.38        92.75        49.91         6.12        26.47        13.38 
TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
        1.55        35.41         8.35        82.39        23.51        65.85 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       35.93        36.72        36.00        91.79        46.75        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-6136 TCGA-AF-A56L 
        9.93        12.00        24.13        17.23        15.39        65.98 
TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 
       11.84        36.03        24.00        34.03        29.98         1.02 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       19.99         1.02         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G 
       36.03        25.97        23.01        12.00        70.03        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 
       38.04         0.49         0.69        10.19         9.37         4.73 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       11.01        12.99        13.97        36.00        30.05       126.44 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 
      129.27         0.49        20.55        15.85        11.97        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       32.19         0.69        47.08 

$`1P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47        11.47        43.76        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        42.28        44.91        45.60        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        37.02        34.65        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       30.44        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        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-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         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-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        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-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-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-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-3850 
       15.95        36.95        14.93         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-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-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-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        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-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-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         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         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72        27.42        10.88         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        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        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       61.41        49.41         6.77       100.01        11.74         1.94 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        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        21.99        21.14         2.93 
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        16.01        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-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        12.26        19.59        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 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-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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      107.67        28.21        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 
       55.04        51.75        45.11        39.42        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        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       18.18        19.33        19.33        15.65        12.79        13.05 
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         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        70.03        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       10.39        86.63        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        7.07        20.05         1.02        46.03         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-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.99         0.99        32.98         0.99         0.99        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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       64.01        10.98        51.98        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         1.45         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97        13.97        78.12         7.17        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02        10.98        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         2.40        19.96        20.91        17.00        18.28 
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-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       31.30         0.39         0.66         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.46        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            140.38 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           19.990            19.055 
[1] "0.2 - 129.3 (20.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    90  45
  1P LOSS WILD-TYPE 352 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     90   45
  1P LOSS WILD-TYPE  352  117
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON               90               352
  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        34         1         0
  1P LOSS WILD-TYPE      88        1       31       137         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           6          4         19         17       23
  1P LOSS WILD-TYPE        20         17         60         37       38
                   vv
clus                STAGE IVA STAGE IVB
  1P LOSS MUTATED           4         0
  1P LOSS WILD-TYPE        23         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               34               137
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               4                17
  STAGE IIIB              19                60
  STAGE IIIC              17                37
  STAGE IV                23                38
  STAGE IVA                4                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
  1P LOSS MUTATED     3  21  94  16
  1P LOSS WILD-TYPE  17  86 319  50
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               3                17
  T2              21                86
  T3              94               319
  T4              16                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
  1P LOSS MUTATED    60  38  36
  1P LOSS WILD-TYPE 282 111  78
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              60               282
  N1              38               111
  N2              36                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    91  28
  1P LOSS WILD-TYPE 357  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     91   28
  1P LOSS WILD-TYPE  357   58
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              91               357
  1              28                58
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    59  76
  1P LOSS WILD-TYPE 227 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     59   76
  1P LOSS WILD-TYPE  227  246
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              59               227
  MALE                76               246
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                     81                             9
  1P LOSS WILD-TYPE                  300                            51
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                      44                              0
  1P LOSS WILD-TYPE                   102                             13
D42V9, multiclass
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        81               300
  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"
D42V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3 132
  1P LOSS WILD-TYPE   6 467
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3  132
  1P LOSS WILD-TYPE    6  467
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                 6
  YES             132               467
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    89   1  10   5
  1P LOSS WILD-TYPE 350   4  26  24
D42V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              89               350
  R1               1                 4
  R2              10                26
  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                          16    66
  1P LOSS WILD-TYPE                        44   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                     16                44
  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"

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    57  16
  1Q LOSS WILD-TYPE 411  99
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               73               510 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16                99 
$`1Q LOSS MUTATED`
TCGA-A6-5660 TCGA-A6-6138 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3562 
       29.19        22.52        38.99         9.07        37.05        19.99 
TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3867 
       50.04        10.06        38.99        37.02        33.07        24.03 
TCGA-AA-3966 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6890 
        2.01         7.96        15.02        33.04        41.00         0.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 
       22.42         0.20        16.44        16.31         5.65         5.13 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CK-6748 TCGA-CM-4750 
       29.56         5.23         3.19         2.14         2.01         8.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       13.02        22.03        29.03        13.02        15.02        11.08 
TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A285 TCGA-DM-A28A 
       10.06        17.75        13.41        11.38         6.12        26.47 
TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50U 
        1.55         8.35        36.72        36.00        91.79        10.98 
TCGA-NH-A8F8 TCGA-AF-2687 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3584 
       12.00        24.13        65.98        11.84        36.03        24.00 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
        1.02        19.99         1.02         1.02        48.03        19.99 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-BM-6198 TCGA-CI-6624 
       36.03        25.97        23.01        12.00        10.19         4.73 
TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 
       12.99        36.00         0.49        15.85        11.97        28.57 
TCGA-G5-6572 
       47.08 

$`1Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        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-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-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-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-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-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-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
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-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-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        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-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-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-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37         4.21        56.55         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       10.88         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        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        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94        83.80        22.36        65.00        62.79        61.41 
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         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
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-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       19.43       107.67        28.21        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        39.42        35.93        26.43        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        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       13.05        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        9.70        30.28        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-4110 
       13.55        19.10        12.72        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 
       16.83        15.39        20.02        10.39        86.63        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       12.00        32.02         8.02         7.07        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        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-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 
       29.98        32.98         0.99         0.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       13.02        35.01        14.01        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        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         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72        26.43         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       11.01        15.02        12.00        13.97        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         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-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-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-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         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-G5-6641 
        1.12         0.76         0.46        18.28        55.76        26.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              0.2               0.0 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.79            140.38 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.85             19.33 
[1] "0.2 - 91.8 (15.8)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1.5"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    51  25
  1Q LOSS WILD-TYPE 391 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     51   25
  1Q LOSS WILD-TYPE  391  137
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON               51               391
  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        18         1         0
  1Q LOSS WILD-TYPE      93        1       34       153         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           4          3          7          8       14
  1Q LOSS WILD-TYPE        22         18         72         46       47
                   vv
clus                STAGE IVA STAGE IVB
  1Q LOSS MUTATED           3         0
  1Q LOSS WILD-TYPE        24         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               18               153
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                4                22
  STAGE IIIA               3                18
  STAGE IIIB               7                72
  STAGE IIIC               8                46
  STAGE IV                14                47
  STAGE IVA                3                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
  1Q LOSS MUTATED     2  14  52   7
  1Q LOSS WILD-TYPE  18  93 361  59
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               2                18
  T2              14                93
  T3              52               361
  T4               7                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
  1Q LOSS MUTATED    35  21  19
  1Q LOSS WILD-TYPE 307 128  95
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              35               307
  N1              21               128
  N2              19                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"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    48  17
  1Q LOSS WILD-TYPE 400  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     48   17
  1Q LOSS WILD-TYPE  400   69
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              48               400
  1              17                69
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    29  47
  1Q LOSS WILD-TYPE 257 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     29   47
  1Q LOSS WILD-TYPE  257  275
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              29               257
  MALE                47               275
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                     45                             6
  1Q LOSS WILD-TYPE                  336                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                      25                              0
  1Q LOSS WILD-TYPE                   121                             13
D43V9, multiclass
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        45               336
  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"
D43V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  74
  1Q LOSS WILD-TYPE   7 525
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   74
  1Q LOSS WILD-TYPE    7  525
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2                 7
  YES              74               525
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    50   1   6   3
  1Q LOSS WILD-TYPE 389   4  30  26
D43V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              50               389
  R1               1                 4
  R2               6                30
  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                          11    35
  1Q LOSS WILD-TYPE                        49   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                     11                49
  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"

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    13   2
  2P LOSS WILD-TYPE 455 113
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               568 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               113 
$`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-3999 TCGA-AG-4001 TCGA-AG-A00H 
       15.39        32.02        36.03        28.04        36.03        25.97 
TCGA-AG-A02X TCGA-EF-5831 TCGA-F5-6571 
       41.00         2.40        31.30 

$`2P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-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-3519 
       63.98         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-3667 
       61.02        78.08         6.05         6.97        54.02        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-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-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-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-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        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21        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        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84        75.25        50.37        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        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        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         1.94         2.24         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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-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        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        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 
       35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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        47.15        52.80        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 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30         9.70        30.28        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        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39        14.50        16.83        20.02        10.39        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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        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-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         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         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         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-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-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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        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         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       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            140.38 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           25.970            19.055 
[1] "2.0 - 41.0 (26.0)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6  11
  2P LOSS WILD-TYPE 436 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6   11
  2P LOSS WILD-TYPE  436  151
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON                6               436
  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       162        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         20         78         52       60
                   vv
clus                STAGE IVA STAGE IVB
  2P LOSS MUTATED           0         0
  2P LOSS WILD-TYPE        27         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               162
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               1                20
  STAGE IIIB               1                78
  STAGE IIIC               2                52
  STAGE IV                 1                60
  STAGE IVA                0                27
  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  20 105 399  65
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                20
  T2               2               105
  T3              14               399
  T4               1                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
  2P LOSS MUTATED    11   4   2
  2P LOSS WILD-TYPE 331 145 112
D44V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              11               331
  N1               4               145
  N2               2               112
[1] 3 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 433  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15    1
  2P LOSS WILD-TYPE  433   85
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              15               433
  1               1                85
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  10
  2P LOSS WILD-TYPE 279 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   10
  2P LOSS WILD-TYPE  279  312
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               279
  MALE                10               312
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                      6                             0
  2P LOSS WILD-TYPE                  375                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                       9                              1
  2P LOSS WILD-TYPE                   137                             12
D44V9, multiclass
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         6               375
  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"
D44V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  16
  2P LOSS WILD-TYPE   8 583
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   16
  2P LOSS WILD-TYPE    8  583
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 8
  YES              16               583
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    14   0   1   0
  2P LOSS WILD-TYPE 425   5  35  29
D44V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              14               425
  R1               0                 5
  R2               1                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"
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                        60   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                60
  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"

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    11   1
  2Q LOSS WILD-TYPE 457 114
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               571 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               114 
$`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-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A02X TCGA-F5-6571 
        3.29        28.04        36.03        25.97        41.00        31.30 

$`2Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-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-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        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-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        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-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-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-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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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 
        4.21        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-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
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         1.94         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-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        13.51        11.51 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        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 
       51.75        45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        9.70        30.28        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        12.72        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-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-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        19.99        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        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         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         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        37.51 
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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.01              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            41.00            140.38 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           27.005            19.040 
[1] "2.0 - 41.0 (27.0)"  "0.0 - 140.4 (19.0)"
[1] "hr=" "2.1"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   7
  2Q LOSS WILD-TYPE 435 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    7
  2Q LOSS WILD-TYPE  435  155
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON                7               435
  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       163        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         20         79         52       61
                   vv
clus                STAGE IVA STAGE IVB
  2Q LOSS MUTATED           0         0
  2Q LOSS WILD-TYPE        27         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               163
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               1                20
  STAGE IIIB               0                79
  STAGE IIIC               2                52
  STAGE IV                 0                61
  STAGE IVA                0                27
  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  20 105 402  65
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                20
  T2               2               105
  T3              11               402
  T4               1                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
  2Q LOSS MUTATED    10   2   2
  2Q LOSS WILD-TYPE 332 147 112
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               332
  N1               2               147
  N2               2               112
[1] 3 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 434  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14    0
  2Q LOSS WILD-TYPE  434   86
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              14               434
  1               0                86
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   9
  2Q LOSS WILD-TYPE 281 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    9
  2Q LOSS WILD-TYPE  281  313
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5               281
  MALE                 9               313
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                      7                             0
  2Q LOSS WILD-TYPE                  374                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                       6                              0
  2Q LOSS WILD-TYPE                   140                             13
D45V9, multiclass
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         7               374
  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"
D45V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  14
  2Q LOSS WILD-TYPE   9 585
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   14
  2Q LOSS WILD-TYPE    9  585
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 9
  YES              14               585
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   0
  2Q LOSS WILD-TYPE 426   5  36  29
D45V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               426
  R1               0                 5
  R2               0                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"
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                        60   291
D45V13, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               363 
       TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H        TCGA-A6-2671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683        TCGA-A6-2684 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807        TCGA-A6-3810 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-4105        TCGA-A6-4107        TCGA-A6-5656        TCGA-A6-5657 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-A566        TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6889 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899        TCGA-AD-6901 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965        TCGA-AD-A5EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-A5EK        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-A69D        TCGA-AY-A71X        TCGA-AY-A8YK        TCGA-AZ-4308 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4614 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4615        TCGA-AZ-4616        TCGA-AZ-4681        TCGA-AZ-4682 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4684        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4951        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4750        TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5341 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A280        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A288 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28A        TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K        TCGA-DM-A28M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6461        TCGA-F4-6463 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6294        TCGA-G4-6295        TCGA-G4-6297 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6298        TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6311        TCGA-G4-6314        TCGA-G4-6315 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6320        TCGA-G4-6321        TCGA-G4-6322 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6323        TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6626        TCGA-G4-6627        TCGA-G4-6628        TCGA-NH-A50T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A50U        TCGA-NH-A50V        TCGA-NH-A5IV        TCGA-NH-A6GA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A6GB        TCGA-NH-A6GC        TCGA-NH-A8F7        TCGA-NH-A8F8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5YV        TCGA-QG-A5YW        TCGA-QG-A5YX        TCGA-QG-A5Z1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5Z2        TCGA-QL-A97D        TCGA-RU-A8FL        TCGA-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" 

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    50  13
  3P LOSS WILD-TYPE 418 102
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               63               520 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               13               102 
$`3P LOSS MUTATED`
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-6142 TCGA-A6-6651 
       34.65        36.53        14.53        32.45        25.08        21.76 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3680 
        9.63         5.03        38.99         9.07         6.05        11.01 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3870 
       85.05        10.06        32.05        31.07        17.03        29.98 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 
       12.99         2.01        21.99        24.00         7.96        13.94 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4614 
       32.02        31.00        16.44        14.50         0.20         5.65 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 
       12.10         3.29         0.26         2.01         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       14.04        11.08        11.01        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 
       43.27        17.85        13.41        11.38         7.50        13.38 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 
        9.93        42.77        30.28        12.72        14.50        20.05 
TCGA-AG-3584 TCGA-AG-3731 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-6682 
       24.00         1.02         0.49        10.19         6.05        13.05 
TCGA-DT-5265 TCGA-F5-6810 TCGA-G5-6233 
        5.29         0.39        18.28 

$`3P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-5656 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-A6-6652 
       24.13         8.38        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-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-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         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-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-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        15.02         5.98        37.05        19.00 
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-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-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        27.02        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-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-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02        19.07        27.02        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-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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         4.21        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-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 
       15.75        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        75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       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         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        49.08        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       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-5863 TCGA-CM-5864 
       22.98        30.08        16.01        15.02        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-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        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        13.51        11.51        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 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-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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        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 
       35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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        47.15        52.80        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        19.33        19.33        15.65        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.00        29.46        32.98         8.42        31.30         9.70 
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-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        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-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
       32.02         8.02         7.07        36.03         1.02        46.03 
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-3728 
       15.95        19.99        19.99         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         0.99        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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00        10.98        30.05        12.95        10.06 
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        37.51        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 
        0.46        55.76        47.08        26.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              0.2               0.0 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            85.05            140.38 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.38             19.99 
[1] "0.2 - 85.0 (13.4)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    52  14
  3P LOSS WILD-TYPE 390 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     52   14
  3P LOSS WILD-TYPE  390  148
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON               52               390
  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        20         0         1
  3P LOSS WILD-TYPE      99        1       35       151        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           4          1         10          6       13
  3P LOSS WILD-TYPE        22         20         69         48       48
                   vv
clus                STAGE IVA STAGE IVB
  3P LOSS MUTATED           5         0
  3P LOSS WILD-TYPE        22         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               20               151
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                4                22
  STAGE IIIA               1                20
  STAGE IIIB              10                69
  STAGE IIIC               6                48
  STAGE IV                13                48
  STAGE IVA                5                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
  3P LOSS MUTATED     2   4  52   9
  3P LOSS WILD-TYPE  18 103 361  57
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                18
  T2               4               103
  T3              52               361
  T4               9                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
  3P LOSS MUTATED    28  21  18
  3P LOSS WILD-TYPE 314 128  96
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              28               314
  N1              21               128
  N2              18                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"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    41  18
  3P LOSS WILD-TYPE 407  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     41   18
  3P LOSS WILD-TYPE  407   68
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              41               407
  1              18                68
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    28  39
  3P LOSS WILD-TYPE 258 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     28   39
  3P LOSS WILD-TYPE  258  283
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              28               258
  MALE                39               283
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                     48                             4
  3P LOSS WILD-TYPE                  333                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                      10                              3
  3P LOSS WILD-TYPE                   136                             10
D46V9, multiclass
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        48               333
  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"
D46V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  65
  3P LOSS WILD-TYPE   7 534
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   65
  3P LOSS WILD-TYPE    7  534
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2                 7
  YES              65               534
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    46   0   8   4
  3P LOSS WILD-TYPE 393   5  28  25
D46V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              46               393
  R1               0                 5
  R2               8                28
  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                           6    32
  3P LOSS WILD-TYPE                        54   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                      6                54
  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"

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    34   8
  3Q LOSS WILD-TYPE 434 107
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               541 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               107 
$`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-AY-6196 TCGA-AZ-6600 TCGA-CA-6716 
       13.94        32.02        16.44         0.20        12.10         0.26 
TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       13.02         5.03        11.08        11.01        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA 
        1.32        43.27        17.85        13.41        11.38         7.50 
TCGA-F4-6460 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 
       13.38        42.77        30.28        12.72        14.50        32.02 
TCGA-AG-3583 TCGA-AG-3731 TCGA-BM-6198 TCGA-CI-6619 TCGA-DT-5265 TCGA-G5-6233 
       20.05         1.02        10.19         6.05         5.29        18.28 

$`3Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 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-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-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         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-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         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-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-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-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-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-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        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-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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         4.21        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-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        15.75        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        75.25        50.37        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41        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         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       19.59        13.51        11.51        20.42        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-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-F4-6461 
       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 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        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 
       51.75        45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.00        29.46        32.98         8.42        31.30         9.70 
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-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        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-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        24.00         1.02        46.03 
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-3728 
       15.95        19.99        19.99         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         0.99        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 
        0.49         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       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        37.51 
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-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              0.2               0.0 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            85.05            140.38 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           13.395            19.660 
[1] "0.2 - 85.0 (13.4)"  "0.0 - 140.4 (19.7)"
[1] "hr=" "1.4"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    33   9
  3Q LOSS WILD-TYPE 409 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     33    9
  3Q LOSS WILD-TYPE  409  153
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON               33               409
  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        15         0         1
  3Q LOSS WILD-TYPE     101        1       35       156        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         21         73         51       52
                   vv
clus                STAGE IVA STAGE IVB
  3Q LOSS MUTATED           3         0
  3Q LOSS WILD-TYPE        24         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               15               156
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               0                21
  STAGE IIIB               6                73
  STAGE IIIC               3                51
  STAGE IV                 9                52
  STAGE IVA                3                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
  3Q LOSS MUTATED     0   3  34   6
  3Q LOSS WILD-TYPE  20 104 379  60
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                20
  T2               3               104
  T3              34               379
  T4               6                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
  3Q LOSS MUTATED    21  11  11
  3Q LOSS WILD-TYPE 321 138 103
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              21               321
  N1              11               138
  N2              11               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"
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    26  11
  3Q LOSS WILD-TYPE 422  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     26   11
  3Q LOSS WILD-TYPE  422   75
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              26               422
  1              11                75
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    16  27
  3Q LOSS WILD-TYPE 270 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16   27
  3Q LOSS WILD-TYPE  270  295
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              16               270
  MALE                27               295
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                     30                             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
D47V9, multiclass
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        30               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"
D47V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  41
  3Q LOSS WILD-TYPE   7 558
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   41
  3Q LOSS WILD-TYPE    7  558
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                 7
  YES              41               558
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    31   0   5   2
  3Q LOSS WILD-TYPE 408   5  31  27
D47V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              31               408
  R1               0                 5
  R2               5                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"
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                           5    20
  3Q LOSS WILD-TYPE                        55   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                      5                55
  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"

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   142  38
  4P LOSS WILD-TYPE 326  77
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              180               403 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38                77 
$`4P LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
        4.80        43.76        43.43        44.91        35.11        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       16.57        37.05        37.02        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       29.16        25.18        21.76        23.87        20.28        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
        9.63         5.03         7.04        38.99        37.05        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       29.00        26.01        21.01        13.02        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
        2.01        50.04        15.02        37.05        36.00        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-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-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       29.98         2.01        12.99        20.98         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F 
       50.99        26.01        34.03        42.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       31.00        33.04        26.01         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 
       41.00         5.79        22.42         0.20        14.50         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 
       15.75         0.20        17.85         5.65         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 TCGA-CK-5912 
       12.10        29.56         3.19         2.14         3.29        49.08 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
        8.02        29.06        22.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       29.03        13.02        15.02        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       10.06        45.40        13.51        20.19        17.75         1.32 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 
       14.30         9.04        13.41        11.38        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6807 
        7.50        44.32         6.12        14.04        26.47        16.24 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 
       33.67        35.41         8.35        23.51        45.11        36.72 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV 
       91.79        46.75        18.18        10.98        12.00        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 
       29.46         9.70        24.13        17.23        43.04        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3593 
       37.74        14.50        15.39        65.98        36.03        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 
        6.05        19.99        29.98         1.02        32.98         1.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       14.04        13.94        25.97        23.01        12.00        70.03 
TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       41.00         0.69        10.19         6.05         6.05         4.73 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA 
       12.99        15.02        36.00        10.98        30.05       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
      129.27        32.61         2.40        15.85        16.34        16.41 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
       11.97        31.30        28.57         0.39         0.69        26.43 

$`4P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
       11.47        11.47        43.76        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       42.28        45.60        37.25        34.65        36.53        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       16.24        24.92        56.25         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-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        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-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       54.02        14.01         0.92        47.05        47.01        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-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       26.01        24.00         2.01        34.03        16.08        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-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-A01G 
       14.99        21.99        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
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-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         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        16.31        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        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41        32.94        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41         6.77       100.01         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.03        12.26        19.59        11.51        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6927 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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76       139.17        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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
        1.55        16.31        29.59        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        39.42        35.93 
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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        47.15        52.80        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.79        13.05        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       30.28        70.03        39.48        13.55        19.10        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        10.39        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 
       19.99        36.95        17.03        13.02        14.01        32.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02        17.03         0.99        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       15.95        36.03         9.07         1.02        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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         0.49         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        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       11.01        15.02        12.00        13.97        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
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-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       17.46         8.45         9.96        37.51        32.19         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              0.2               0.0 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           140.38            139.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            20.09             19.04 
[1] "0.2 - 140.4 (20.1)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   132  58
  4P LOSS WILD-TYPE 310 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    132   58
  4P LOSS WILD-TYPE  310  104
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON              132               310
  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        49         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          9         25         22       30
  4P LOSS WILD-TYPE        19         12         54         32       31
                   vv
clus                STAGE IVA STAGE IVB
  4P LOSS MUTATED          11         1
  4P LOSS WILD-TYPE        16         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               49               122
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                7                19
  STAGE IIIA               9                12
  STAGE IIIB              25                54
  STAGE IIIC              22                32
  STAGE IV                30                31
  STAGE IVA               11                16
  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  30 132  24
  4P LOSS WILD-TYPE  14  77 281  42
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               6                14
  T2              30                77
  T3             132               281
  T4              24                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
  4P LOSS MUTATED    88  56  48
  4P LOSS WILD-TYPE 254  93  66
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              88               254
  N1              56                93
  N2              48                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   126  41
  4P LOSS WILD-TYPE 322  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    126   41
  4P LOSS WILD-TYPE  322   45
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             126               322
  1              41                45
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    88 104
  4P LOSS WILD-TYPE 198 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     88  104
  4P LOSS WILD-TYPE  198  218
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              88               198
  MALE               104               218
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                    122                            10
  4P LOSS WILD-TYPE                  259                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                      54                              3
  4P LOSS WILD-TYPE                    92                             10
D48V9, multiclass
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       122               259
  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"
D48V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     8 184
  4P LOSS WILD-TYPE   1 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8  184
  4P LOSS WILD-TYPE    1  415
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                8                 1
  YES             184               415
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   138   0  15   6
  4P LOSS WILD-TYPE 301   5  21  23
D48V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             138               301
  R1               0                 5
  R2              15                21
  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                          20    90
  4P LOSS WILD-TYPE                        40   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                     20                40
  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"

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   139  35
  4Q LOSS WILD-TYPE 329  80
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              174               409 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               35                80 
$`4Q LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
        4.80        43.76        43.43        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-6654 
       37.05        32.45        29.19        29.16        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3522 
       20.28        61.84         9.63         5.03        38.99        37.05 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       34.03        29.00        26.01        33.99        21.01        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 
       19.99         6.05         2.01        50.04        37.05        36.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 
       10.06        33.07         0.99        31.07        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       20.98         2.01        21.99        50.99        26.01        24.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X 
       34.03        42.02        15.02        32.02        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
        2.96        39.98        41.00         5.79        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
       14.50        16.31         0.95         0.20        17.85         5.65 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-6719 
        5.13        65.00        12.10        29.56         2.14         1.35 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       49.08         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.01        11.08        11.01        45.40        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D9 
       17.75         1.32        43.27         9.04        13.41       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 
        7.50        44.32         6.12        14.04        26.47        13.38 
TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 
       16.24        35.41         8.35        23.51        45.11        36.72 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 
       91.79        46.75        18.18        10.98         9.93        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       42.77        29.46         9.70        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        12.72        37.74        14.50        15.39 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
       65.98        36.03        34.03         6.05        19.99        29.98 
TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       32.98         1.02         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       36.03        14.04        13.94        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       70.03        64.01        41.00         0.49         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
        6.05         6.05         4.73        11.01        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 
       36.00        10.98        30.05       126.44       129.27         2.40 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 
       17.00        15.85        16.34        16.41        11.97        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57         0.39        32.19         0.66         0.69        26.43 

$`4Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
       11.47        11.47        43.76        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        44.91        45.60        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       56.25         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-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
        0.00        19.07        29.00        12.99         0.99        14.01 
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-3667 
       13.94        61.02        78.08         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-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       19.00         5.03        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-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
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-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-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        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-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
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-6890 
       40.96         0.07        21.37         4.21        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-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        15.75        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        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        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         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-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-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       19.59        11.51        20.42        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76       139.17        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        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       16.31        29.59        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        39.42        35.93 
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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       26.17        47.15        52.80        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       12.79        13.05        32.98         8.42        31.30        30.28 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       70.03        39.48        10.39        16.83        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        7.07        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        0.99         1.02         0.99         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4007 
       17.03        13.02        35.01        14.01        32.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
       17.03         0.99        20.98         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.72        26.43         1.81         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       78.12         7.17        10.98        15.02        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
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-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       20.91        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        37.51 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              0.2               0.0 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.38            139.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           19.545            19.070 
[1] "0.2 - 140.4 (19.5)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.1"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   119  62
  4Q LOSS WILD-TYPE 323 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    119   62
  4Q LOSS WILD-TYPE  323  100
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON              119               323
  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        49         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          8         27         25       23
  4Q LOSS WILD-TYPE        19         13         52         29       38
                   vv
clus                STAGE IVA STAGE IVB
  4Q LOSS MUTATED          10         0
  4Q LOSS WILD-TYPE        17         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               49               122
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                7                19
  STAGE IIIA               8                13
  STAGE IIIB              27                52
  STAGE IIIC              25                29
  STAGE IV                23                38
  STAGE IVA               10                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
  4Q LOSS MUTATED     5  29 127  24
  4Q LOSS WILD-TYPE  15  78 286  42
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                15
  T2              29                78
  T3             127               286
  T4              24                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
  4Q LOSS MUTATED    85  56  44
  4Q LOSS WILD-TYPE 257  93  70
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              85               257
  N1              56                93
  N2              44                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   126  33
  4Q LOSS WILD-TYPE 322  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    126   33
  4Q LOSS WILD-TYPE  322   53
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             126               322
  1              33                53
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    85 100
  4Q LOSS WILD-TYPE 201 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     85  100
  4Q LOSS WILD-TYPE  201  222
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              85               201
  MALE               100               222
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                    108                            11
  4Q LOSS WILD-TYPE                  273                            49
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                      58                              3
  4Q LOSS WILD-TYPE                    88                             10
D49V9, multiclass
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       108               273
  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"
D49V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 177
  4Q LOSS WILD-TYPE   1 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  177
  4Q LOSS WILD-TYPE    1  422
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                8                 1
  YES             177               422
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   133   1  11   7
  4Q LOSS WILD-TYPE 306   4  25  22
D49V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             133               306
  R1               1                 4
  R2              11                25
  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                          21    91
  4Q LOSS WILD-TYPE                        39   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                     21                39
  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"

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    60  18
  5P LOSS WILD-TYPE 408  97
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               78               505 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               18                97 
$`5P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-3810 TCGA-A6-4105 
       43.76        43.76        42.28        13.94        36.53        14.53 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6654 
       29.19        32.71        27.09        25.18        24.16        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3841 
        9.63         5.03        26.01        50.04        10.06        36.95 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00F 
       10.06        33.07        36.03        24.00         2.01        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6901 
       27.02        42.02        10.98        33.04        41.00        22.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
        0.20        16.31        17.26         5.65        65.00        62.79 
TCGA-AZ-6605 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        5.23        49.08         8.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6922 
       15.02        14.04        29.03        11.01        17.85        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U 
       12.43         9.04         8.35        36.00        18.18        10.98 
TCGA-QG-A5YV TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3600 
       42.77         9.70        24.13        43.04        15.39         6.05 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y 
        1.02        19.99         1.02        48.03        28.04        23.01 
TCGA-AG-A01W TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA 
       70.03         6.05        13.97        36.00        10.98       126.44 
TCGA-DY-A1DD TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7004 TCGA-G5-6233 
       57.24        20.55        16.41        13.64         8.45        18.28 

$`5P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       24.33        44.91        35.11        45.60        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        34.65        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 
       30.44        33.53        23.61        22.09        22.06        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13         8.38        25.08        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-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-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-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-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-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        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-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.00         0.00        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-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        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        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-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         4.21        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-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        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        75.25        50.37        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        83.80        22.36        61.41 
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         1.94         2.24         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         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        16.01        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        13.51        11.51        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         7.53        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       52.80        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 
       13.05        12.00        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       30.28        70.03        39.48        17.23        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
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-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       17.03        13.02        35.01        14.01        32.02        19.99 
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         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        31.00        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         0.49         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-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.99        12.00        15.02        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36       129.27        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-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-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46        11.97         9.96        37.51 
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-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.2               0.0 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            140.38 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            21.29             19.04 
[1] "0.2 - 126.4 (21.3)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.2"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    57  27
  5P LOSS WILD-TYPE 385 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     57   27
  5P LOSS WILD-TYPE  385  135
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON               57               385
  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        14         0         2
  5P LOSS WILD-TYPE      89        1       32       157        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           4          6         11         11        7
  5P LOSS WILD-TYPE        22         15         68         43       54
                   vv
clus                STAGE IVA STAGE IVB
  5P LOSS MUTATED           8         0
  5P LOSS WILD-TYPE        19         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               14               157
  STAGE IIB                0                10
  STAGE IIC                2                 1
  STAGE III                4                22
  STAGE IIIA               6                15
  STAGE IIIB              11                68
  STAGE IIIC              11                43
  STAGE IV                 7                54
  STAGE IVA                8                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
  5P LOSS MUTATED     3  15  55  11
  5P LOSS WILD-TYPE  17  92 358  55
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               3                17
  T2              15                92
  T3              55               358
  T4              11                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
  5P LOSS MUTATED    37  27  20
  5P LOSS WILD-TYPE 305 122  94
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              37               305
  N1              27               122
  N2              20                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"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    59  14
  5P LOSS WILD-TYPE 389  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     59   14
  5P LOSS WILD-TYPE  389   72
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              59               389
  1              14                72
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    43  41
  5P LOSS WILD-TYPE 243 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     43   41
  5P LOSS WILD-TYPE  243  281
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              43               243
  MALE                41               281
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                     52                             5
  5P LOSS WILD-TYPE                  329                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                      26                              1
  5P LOSS WILD-TYPE                   120                             12
D50V9, multiclass
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        52               329
  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"
D50V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4  80
  5P LOSS WILD-TYPE   5 519
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   80
  5P LOSS WILD-TYPE    5  519
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4                 5
  YES              80               519
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    57   1   3   3
  5P LOSS WILD-TYPE 382   4  33  26
D50V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              57               382
  R1               1                 4
  R2               3                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"
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                           9    47
  5P LOSS WILD-TYPE                        51   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                      9                51
  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"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    82  30
  5Q LOSS WILD-TYPE 386  85
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              112               471 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               30                85 
$`5Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       43.76        43.76        13.94        37.02        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       30.44        29.19        27.09        25.18        24.16        21.76 
TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 
       23.87         9.63         5.03        26.01        12.99        13.02 
TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3848 
       19.99        50.04        85.05        10.06        36.95        10.06 
TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       33.07        31.07        24.03        24.00         2.01        21.99 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02H 
       34.03        27.02        42.02        10.98        33.04         2.01 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       41.00        22.42        27.42         0.20        16.31         0.20 
TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-AZ-6608 
       17.26         5.65        65.00        62.79         5.23         1.94 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5862 
        3.29         1.35        49.08         8.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6536 TCGA-D5-6922 
       15.02        14.04        29.03        13.02        17.85        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6459 
       12.43         9.04        13.41        44.32         6.12         8.61 
TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T 
        1.55         8.35        82.39        36.00        91.79        18.18 
TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 
       10.98        42.77         9.70        30.28        24.13        17.23 
TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AG-3578 TCGA-AG-3728 
       43.04        37.74        15.39        86.63        32.02        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
        1.02        32.98        19.99         1.02        48.03        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 
       36.03        17.03        23.01        70.03        64.01         1.94 
TCGA-AG-A02G TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       38.96        10.19         6.05        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG 
       36.00        10.98        13.05       126.44        57.24        51.48 
TCGA-EI-6506 TCGA-EI-6881 TCGA-F5-6702 TCGA-G5-6233 
       20.55        16.41        28.57        18.28 

$`5Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       24.33        42.28        44.91        35.11        45.60        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-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       22.52        24.13         8.38        25.08        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-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84        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-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-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-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-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-3854 TCGA-AA-3855 
        0.00        17.03         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        53.00        17.03        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-3971 TCGA-AA-3972 
       24.00         2.01        20.98        34.03        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-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        38.04         4.01         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        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         5.79        10.88        16.44 
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        15.75 
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        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56        11.74         3.19         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.25         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        16.01        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-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        13.51        11.51        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         7.53        12.39        14.30 
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-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-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
       35.97        60.79       117.07        98.24        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.72        26.43        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        47.15        52.80 
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        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       12.00        29.46        32.98         8.42        31.30        70.03 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        13.55        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        10.39        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 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-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99         0.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 
       13.02        35.01        14.01        32.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.98        13.94         6.02        25.97 
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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       31.00        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       78.12         7.17        10.98        11.01        15.02        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE 
       30.05        12.95        10.06         5.29        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49         2.40        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-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        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         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.2               0.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            140.38 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           21.875            19.000 
[1] "0.2 - 126.4 (21.9)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.4"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    78  41
  5Q LOSS WILD-TYPE 364 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     78   41
  5Q LOSS WILD-TYPE  364  121
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON               78               364
  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        26         0         1
  5Q LOSS WILD-TYPE      86        1       30       145        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           4          6         15         17       13
  5Q LOSS WILD-TYPE        22         15         64         37       48
                   vv
clus                STAGE IVA STAGE IVB
  5Q LOSS MUTATED          10         0
  5Q LOSS WILD-TYPE        17         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               26               145
  STAGE IIB                0                10
  STAGE IIC                1                 2
  STAGE III                4                22
  STAGE IIIA               6                15
  STAGE IIIB              15                64
  STAGE IIIC              17                37
  STAGE IV                13                48
  STAGE IVA               10                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
  5Q LOSS MUTATED     3  19  85  12
  5Q LOSS WILD-TYPE  17  88 328  54
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               3                17
  T2              19                88
  T3              85               328
  T4              12                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
  5Q LOSS MUTATED    55  31  33
  5Q LOSS WILD-TYPE 287 118  81
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              55               287
  N1              31               118
  N2              33                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"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    79  23
  5Q LOSS WILD-TYPE 369  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     79   23
  5Q LOSS WILD-TYPE  369   63
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              79               369
  1              23                63
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    54  65
  5Q LOSS WILD-TYPE 232 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     54   65
  5Q LOSS WILD-TYPE  232  257
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              54               232
  MALE                65               257
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                     71                             7
  5Q LOSS WILD-TYPE                  310                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                      39                              1
  5Q LOSS WILD-TYPE                   107                             12
D51V9, multiclass
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        71               310
  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"
D51V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     6 113
  5Q LOSS WILD-TYPE   3 486
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6  113
  5Q LOSS WILD-TYPE    3  486
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                6                 3
  YES             113               486
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    80   2   7   4
  5Q LOSS WILD-TYPE 359   3  29  25
D51V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              80               359
  R1               2                 3
  R2               7                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"
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                          13    59
  5Q LOSS WILD-TYPE                        47   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                     13                47
  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"

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    30  12
  6P LOSS WILD-TYPE 438 103
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               42               541 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               103 
$`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         2.24         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         7.53 
TCGA-DM-A1D7 TCGA-F4-6808 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3593 
       13.32        33.67        17.23        13.55        12.72        34.03 
TCGA-AG-A008 TCGA-AG-A011 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6883 
       13.94        37.02        13.05         5.29        24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        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-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        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-3696 
       15.02        11.01         5.98        37.05        19.00         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-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        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-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        31.00         2.01 
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-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-A00K 
       13.94        38.04        19.00        30.02        34.03        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        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        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-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        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-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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         1.94 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 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-D5-6530 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.42        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05        12.00 
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         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       30.28        70.03        24.13        39.48        43.04        19.10 
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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         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-3882 
       29.98         1.02        32.98         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-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-A00C 
       14.04         1.02        17.03         0.99        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-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         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         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 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       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-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        37.51        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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.01              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            45.40            140.38 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           16.835            19.330 
[1] "2.0 - 45.4 (16.8)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "2.1"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    33  11
  6P LOSS WILD-TYPE 409 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33   11
  6P LOSS WILD-TYPE  409  151
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON               33               409
  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       151         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         21         76         51       58
                   vv
clus                STAGE IVA STAGE IVB
  6P LOSS MUTATED           3         0
  6P LOSS WILD-TYPE        24         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               151
  STAGE IIB                1                 9
  STAGE IIC                1                 2
  STAGE III                2                24
  STAGE IIIA               0                21
  STAGE IIIB               3                76
  STAGE IIIC               3                51
  STAGE IV                 3                58
  STAGE IVA                3                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
  6P LOSS MUTATED     2   6  30   7
  6P LOSS WILD-TYPE  18 101 383  59
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                18
  T2               6               101
  T3              30               383
  T4               7                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
  6P LOSS MUTATED    30   8   7
  6P LOSS WILD-TYPE 312 141 107
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              30               312
  N1               8               141
  N2               7               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"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    34   6
  6P LOSS WILD-TYPE 414  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     34    6
  6P LOSS WILD-TYPE  414   80
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              34               414
  1               6                80
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    19  26
  6P LOSS WILD-TYPE 267 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     19   26
  6P LOSS WILD-TYPE  267  296
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              19               267
  MALE                26               296
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                     28                             5
  6P LOSS WILD-TYPE                  353                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                       8                              3
  6P LOSS WILD-TYPE                   138                             10
D52V9, multiclass
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        28               353
  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"
D52V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  44
  6P LOSS WILD-TYPE   8 555
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   44
  6P LOSS WILD-TYPE    8  555
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 8
  YES              44               555
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    31   0   1   6
  6P LOSS WILD-TYPE 408   5  35  23
D52V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              31               408
  R1               0                 5
  R2               1                35
  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                        59   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                59
  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"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    48  16
  6Q LOSS WILD-TYPE 420  99
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               64               519 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16                99 
$`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         2.24         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         7.53        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-3593 
       12.72        12.00        32.02        24.00        46.03        34.03 
TCGA-AG-3600 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-DC-6682 
        6.05        14.04        13.94        37.02         0.49        13.05 
TCGA-DT-5265 TCGA-EI-6883 TCGA-G5-6233 TCGA-G5-6641 
        5.29        11.51        18.28        26.43 

$`6Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       16.57        37.05        37.25        37.02        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-A6-6650 
       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-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-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-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-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-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 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-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        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-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
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-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-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-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        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-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-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        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        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 
      100.01        29.56         5.23        11.74         1.94         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        10.06        12.03        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        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 
       51.75        45.11        39.42        35.93        36.72        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        47.15        52.80        18.18        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        13.05        12.00 
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         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 
       30.28        70.03        24.13        39.48        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-3580 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       20.05         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98         6.02        25.97        23.01 
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-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-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00        10.98        30.05        12.95        10.06 
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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        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        37.51        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 
        0.46        55.76        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            61.02            140.38 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.58             19.96 
[1] "0.5 - 61.0 (14.6)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    45  21
  6Q LOSS WILD-TYPE 397 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     45   21
  6Q LOSS WILD-TYPE  397  141
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON               45               397
  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       151         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         20         72         45       54
                   vv
clus                STAGE IVA STAGE IVB
  6Q LOSS MUTATED           3         1
  6Q LOSS WILD-TYPE        24         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               151
  STAGE IIB                1                 9
  STAGE IIC                2                 1
  STAGE III                2                24
  STAGE IIIA               1                20
  STAGE IIIB               7                72
  STAGE IIIC               9                45
  STAGE IV                 7                54
  STAGE IVA                3                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
  6Q LOSS MUTATED     4   8  48   8
  6Q LOSS WILD-TYPE  16  99 365  58
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               4                16
  T2               8                99
  T3              48               365
  T4               8                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
  6Q LOSS MUTATED    35  13  20
  6Q LOSS WILD-TYPE 307 136  94
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              35               307
  N1              13               136
  N2              20                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"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    46  12
  6Q LOSS WILD-TYPE 402  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     46   12
  6Q LOSS WILD-TYPE  402   74
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              46               402
  1              12                74
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    27  41
  6Q LOSS WILD-TYPE 259 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27   41
  6Q LOSS WILD-TYPE  259  281
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              27               259
  MALE                41               281
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                     38                             7
  6Q LOSS WILD-TYPE                  343                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                      16                              5
  6Q LOSS WILD-TYPE                   130                              8
D53V9, multiclass
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        38               343
  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"
D53V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  67
  6Q LOSS WILD-TYPE   8 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   67
  6Q LOSS WILD-TYPE    8  532
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 8
  YES              67               532
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    50   0   3   7
  6Q LOSS WILD-TYPE 389   5  33  22
D53V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              50               389
  R1               0                 5
  R2               3                33
  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                        57   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                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"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 465 115
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               580 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0               115 
$`7Q LOSS MUTATED`
TCGA-CM-5341 TCGA-D5-6932 TCGA-AG-A008 
       29.06        11.38        13.94 

$`7Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-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-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-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-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        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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 
        4.21        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-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        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        83.80        22.36        65.00        62.79        61.41 
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         1.94         2.24         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-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        13.51        11.51 
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         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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-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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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        47.15        52.80        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        13.05        12.00 
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         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        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        12.72        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-3593 
       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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
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-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98         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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         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        37.51        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         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       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 
            29.06            140.38 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.94             19.07 
[1] "11.4 - 29.1 (13.9)" "0.0 - 140.4 (19.1)"
[1] "hr="     "1200000"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   2
  7Q LOSS WILD-TYPE 440 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    2
  7Q LOSS WILD-TYPE  440  160
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON                2               440
  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         2         0         0
  7Q LOSS WILD-TYPE     103        1       36       169        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         20         79         54       61
                   vv
clus                STAGE IVA STAGE IVB
  7Q LOSS MUTATED           0         0
  7Q LOSS WILD-TYPE        27         2
D54V4, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 0                36
  STAGE IIA                2               169
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                0                26
  STAGE IIIA               1                20
  STAGE IIIB               0                79
  STAGE IIIC               0                54
  STAGE IV                 0                61
  STAGE IVA                0                27
  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   2   0
  7Q LOSS WILD-TYPE  20 105 411  66
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                20
  T2               2               105
  T3               2               411
  T4               0                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
  7Q LOSS MUTATED     3   1   0
  7Q LOSS WILD-TYPE 339 148 114
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               3               339
  N1               1               148
  N2               0               114
[1] 3 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
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 444  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    0
  7Q LOSS WILD-TYPE  444   86
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               4               444
  1               0                86
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   1
  7Q LOSS WILD-TYPE 283 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE  283  321
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3               283
  MALE                 1               321
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                      2                             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
D54V9, multiclass
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         2               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"
D54V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   4
  7Q LOSS WILD-TYPE   9 595
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    4
  7Q LOSS WILD-TYPE    9  595
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 9
  YES               4               595
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     4   0   0   0
  7Q LOSS WILD-TYPE 435   5  36  29
D54V11, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               4               435
  R1               0                 5
  R2               0                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"
D54V12, 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                           0     2
  7Q LOSS WILD-TYPE                        60   290
D54V13, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               363 
       TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H        TCGA-A6-2671 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683        TCGA-A6-2684 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807        TCGA-A6-3810 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-4105        TCGA-A6-4107        TCGA-A6-5656        TCGA-A6-5657 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-A566        TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6889 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899        TCGA-AD-6901 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965        TCGA-AD-A5EJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-A5EK        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AY-A69D        TCGA-AY-A71X        TCGA-AY-A8YK        TCGA-AZ-4308 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4614 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-4615        TCGA-AZ-4616        TCGA-AZ-4681        TCGA-AZ-4682 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-4684        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4951        TCGA-CK-4952        TCGA-CK-5912 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-4748        TCGA-CM-4750        TCGA-CM-4751        TCGA-CM-4752 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6294        TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6320        TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6627        TCGA-G4-6628        TCGA-NH-A50T        TCGA-NH-A50U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-NH-A50V        TCGA-NH-A5IV        TCGA-NH-A6GA        TCGA-NH-A6GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-NH-A6GC        TCGA-NH-A8F7        TCGA-NH-A8F8        TCGA-QG-A5YV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-QG-A5YW        TCGA-QG-A5YX        TCGA-QG-A5Z1        TCGA-QG-A5Z2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-QL-A97D        TCGA-RU-A8FL        TCGA-WS-AB45        TCGA-AF-2687 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691        TCGA-AF-2692 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911        TCGA-AF-3913 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-6672        TCGA-AF-A56K        TCGA-AF-A56L        TCGA-AF-A56N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6623 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6464 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   165  44
  8P LOSS WILD-TYPE 303  71
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              209               374 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               44                71 
$`8P LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 
        4.80        43.76        43.76        43.43        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        16.57        34.65        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       30.44        23.61        27.09        24.13        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        24.69        23.87        20.28        61.84        56.25 
TCGA-AA-3488 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3529 
        5.03        37.05         1.02        38.99        24.03         0.00 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       34.03        26.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3678 
       23.01        19.99        19.99        78.08         2.01        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-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       85.05        37.02        33.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       27.02         2.01        24.00        34.03        16.08        34.06 
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-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       15.02        12.00        31.00         1.02        33.04        37.02 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       41.00        22.42         0.20        16.31        15.75         0.20 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6600 
       17.85        75.25         5.65        83.80        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         1.94         3.29         1.35        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        16.01         5.03 
TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        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        13.51        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        10.13         9.04        13.41        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        13.38        13.64         1.55        16.31         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        36.72        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        12.00         9.70 
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-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       46.03        34.03         2.01         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98        32.98         0.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       35.01        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02        15.95         1.02        12.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98         1.94        38.96        41.00         1.45 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
        0.72        10.19         4.73        13.97        78.12        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 
       11.01        12.99        13.97        36.00        10.98        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 
        5.29       126.44       129.27        51.48         2.40        15.85 
TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       16.34        10.78        11.97         8.45         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
       28.57         0.69         0.46        18.28        26.43 

$`8P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2682 
       11.47        11.47        46.65        42.90        24.33        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5657 
       37.05        37.25        37.02        14.53        32.45        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       22.52         8.38        24.16        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       19.66        16.24        24.92         9.63         7.04         3.02 
TCGA-AA-3494 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-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        19.07        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       14.01        17.95        29.95        20.98        13.94        61.02 
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-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       47.05         5.03        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-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-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 
       53.00        29.98        18.05        31.00        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        20.98         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       50.99        13.05        25.02        19.07        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-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-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        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         4.21 
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-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-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        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       61.41        49.41         6.77       100.01         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
        8.02        27.02        29.06        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02        12.00        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        19.59        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25         1.32        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14         7.53        12.39        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-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       38.20        92.75        12.59         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24        95.18         8.61        11.11        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        29.59        16.24        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       45.11        39.42        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       26.17        46.75        47.15        52.80        18.18        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        13.05        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3400 
        8.42        31.30        70.03        24.13        43.04        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       14.50        16.83        20.02        86.63        65.98        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-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 
       50.04        12.03        15.95        19.99        19.99         1.02 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        0.99        19.99        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       48.03        32.02         1.02         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        6.02        36.03         9.07        31.00        70.03        64.01 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04         0.49         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 
        1.81         6.05         6.05         6.97         9.37         7.17 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02        30.05        12.95        13.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 
       16.41         8.61        11.51        13.64        17.46        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19         0.66         0.53         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           140.38            139.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           19.330            19.055 
[1] "0.0 - 140.4 (19.3)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   140  73
  8P LOSS WILD-TYPE 302  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    140   73
  8P LOSS WILD-TYPE  302   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON              140               302
  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       120         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED          12         10         28         24       31
  8P LOSS WILD-TYPE        14         11         51         30       30
                   vv
clus                STAGE IVA STAGE IVB
  8P LOSS MUTATED          12         1
  8P LOSS WILD-TYPE        15         1
D55V4, 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               120
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III               12                14
  STAGE IIIA              10                11
  STAGE IIIB              28                51
  STAGE IIIC              24                30
  STAGE IV                31                30
  STAGE IVA               12                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
  8P LOSS MUTATED     3  34 154  24
  8P LOSS WILD-TYPE  17  73 259  42
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                17
  T2              34                73
  T3             154               259
  T4              24                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  54
  8P LOSS WILD-TYPE 243  88  60
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              99               243
  N1              61                88
  N2              54                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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   148  42
  8P LOSS WILD-TYPE 300  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    148   42
  8P LOSS WILD-TYPE  300   44
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             148               300
  1              42                44
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    91 124
  8P LOSS WILD-TYPE 195 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     91  124
  8P LOSS WILD-TYPE  195  198
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              91               195
  MALE               124               198
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                    127                            12
  8P LOSS WILD-TYPE                  254                            48
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                      67                              5
  8P LOSS WILD-TYPE                    79                              8
D55V9, multiclass
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       127               254
  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"
D55V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5 210
  8P LOSS WILD-TYPE   4 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  210
  8P LOSS WILD-TYPE    4  389
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                5                 4
  YES             210               389
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   153   2  16   5
  8P LOSS WILD-TYPE 286   3  20  24
D55V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             153               286
  R1               2                 3
  R2              16                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"
D55V12, 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                          23   100
  8P LOSS WILD-TYPE                        37   192
D55V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 9
  BLACK OR AFRICAN AMERICAN                     23                37
  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"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27   8
  8Q LOSS WILD-TYPE 441 107
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               548 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8               107 
$`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-6196 TCGA-AY-A69D TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6679 
        0.20         0.20        17.85        62.79        16.01        10.06 
TCGA-D5-5538 TCGA-D5-6539 TCGA-DM-A1D6 TCGA-F4-6704 TCGA-G4-6625 TCGA-QL-A97D 
       12.26        12.49        49.91         1.55        91.79         9.70 
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 
       36.00        51.48        15.85         0.69        18.28 

$`8Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       24.33        42.28        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        36.53        14.53        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-A6-6651 
        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-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-3518 TCGA-AA-3519 
       63.98         6.97         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-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        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-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-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-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-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        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        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21        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-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        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        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        61.41        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         1.94         2.24 
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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        45.40        19.59        13.51        11.51 
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-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-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        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        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        47.15        52.80 
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        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        30.28        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        12.72        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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        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-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        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         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        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         0.49         1.45         0.69 
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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         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-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-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        37.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.2               0.0 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.79            140.38 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            18.28             19.07 
[1] "0.2 - 91.8 (18.3)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    24  12
  8Q LOSS WILD-TYPE 418 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     24   12
  8Q LOSS WILD-TYPE  418  150
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON               24               418
  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       161         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         20         76         50       57
                   vv
clus                STAGE IVA STAGE IVB
  8Q LOSS MUTATED           2         0
  8Q LOSS WILD-TYPE        25         2
D56V4, 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               161
  STAGE IIB                2                 8
  STAGE IIC                1                 2
  STAGE III                0                26
  STAGE IIIA               1                20
  STAGE IIIB               3                76
  STAGE IIIC               4                50
  STAGE IV                 4                57
  STAGE IVA                2                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
  8Q LOSS MUTATED     0   5  26   5
  8Q LOSS WILD-TYPE  20 102 387  61
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                20
  T2               5               102
  T3              26               387
  T4               5                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
  8Q LOSS MUTATED    21   5   9
  8Q LOSS WILD-TYPE 321 144 105
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              21               321
  N1               5               144
  N2               9               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"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   6
  8Q LOSS WILD-TYPE 427  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    6
  8Q LOSS WILD-TYPE  427   80
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              21               427
  1               6                80
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  26
  8Q LOSS WILD-TYPE 276 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   26
  8Q LOSS WILD-TYPE  276  296
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               276
  MALE                26               296
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                     20                             4
  8Q LOSS WILD-TYPE                  361                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                      12                              0
  8Q LOSS WILD-TYPE                   134                             13
D56V9, multiclass
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        20               361
  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"
D56V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  36
  8Q LOSS WILD-TYPE   9 563
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   36
  8Q LOSS WILD-TYPE    9  563
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 9
  YES              36               563
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    27   0   1   0
  8Q LOSS WILD-TYPE 412   5  35  29
D56V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              27               412
  R1               0                 5
  R2               1                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"
D56V12, 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                        57   271
D56V13, 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                57
  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"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    56  14
  9P LOSS WILD-TYPE 412 101
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               70               513 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14               101 
$`9P LOSS MUTATED`
TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 
       43.43        36.53        14.53        29.16        24.16        21.76 
TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3685 
       61.84         6.97        38.99        24.00        19.99        37.05 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3972 
       85.05        24.03        12.99        24.00        20.98        50.99 
TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6965 
       13.94        32.02        31.00        40.96         4.21         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       14.50        16.31         5.65         5.23         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
        3.29         0.26         8.02        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6898 
       11.01        10.06        20.19         1.32        43.27         7.53 
TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA TCGA-NH-A8F8 
       38.20        33.67         8.35        82.39         9.93        12.00 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 
       24.13        13.55        65.98        20.05        34.03         6.05 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 
        1.02        19.99        15.95        12.00        31.00         1.94 
TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 
       38.96         6.05         4.73        13.97        11.01        10.98 
TCGA-DC-6160 TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       30.05        51.48         0.49        16.31 

$`9P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
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-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 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-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         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-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-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-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-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        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-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-3947 TCGA-AA-3949 
       29.98        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        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-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        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-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        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-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        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        75.25        50.37 
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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
      100.01        29.56        11.74         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-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        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        15.12        17.85         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        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        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        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       52.80        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        13.05        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         9.70        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        12.72        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-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-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99         0.99         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         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        36.03         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
        1.81        10.19         6.05         6.97         9.37        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        10.98        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        36.00        12.95        13.05        10.06         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-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-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        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 
       37.51        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         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       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            140.38 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           15.485            19.330 
[1] "0.2 - 85.0 (15.5)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    51  22
  9P LOSS WILD-TYPE 391 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51   22
  9P LOSS WILD-TYPE  391  140
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON               51               391
  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        16         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         18         70         46       48
                   vv
clus                STAGE IVA STAGE IVB
  9P LOSS MUTATED           4         0
  9P LOSS WILD-TYPE        23         2
D57V4, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               16               155
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                2                24
  STAGE IIIA               3                18
  STAGE IIIB               9                70
  STAGE IIIC               8                46
  STAGE IV                13                48
  STAGE IVA                4                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
  9P LOSS MUTATED     2  17  42  13
  9P LOSS WILD-TYPE  18  90 371  53
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                18
  T2              17                90
  T3              42               371
  T4              13                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
  9P LOSS MUTATED    37  18  18
  9P LOSS WILD-TYPE 305 131  96
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              37               305
  N1              18               131
  N2              18                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"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    51  17
  9P LOSS WILD-TYPE 397  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51   17
  9P LOSS WILD-TYPE  397   69
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              51               397
  1              17                69
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  45
  9P LOSS WILD-TYPE 257 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   45
  9P LOSS WILD-TYPE  257  277
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29               257
  MALE                45               277
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                     49                             2
  9P LOSS WILD-TYPE                  332                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                      21                              1
  9P LOSS WILD-TYPE                   125                             12
D57V9, multiclass
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        49               332
  COLON MUCINOUS ADENOCARCINOMA                2                58
  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"
D57V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  73
  9P LOSS WILD-TYPE   8 526
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   73
  9P LOSS WILD-TYPE    8  526
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 8
  YES              73               526
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    47   2   8   3
  9P LOSS WILD-TYPE 392   3  28  26
D57V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              47               392
  R1               2                 3
  R2               8                28
  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"
D57V12, 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                           6    37
  9P LOSS WILD-TYPE                        54   255
D57V13, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      6                54
  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"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    55  16
  9Q LOSS WILD-TYPE 413  99
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               71               512 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               16                99 
$`9Q LOSS MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6649 
       43.76        43.43        36.53        29.16        25.08        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-3955 TCGA-AA-3972 
       37.05        85.05        24.03        12.99        20.98        50.99 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A03J TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       32.02        31.00        40.96        14.50        16.31         0.95 
TCGA-AZ-4614 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 
        5.65        29.56         5.23         3.19         1.94         3.29 
TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6169 TCGA-CM-6170 
        0.26         8.02        13.02        22.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6898 
       11.08        11.01        10.06        20.19         1.32         7.53 
TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-NH-A6GA 
       38.20        33.67         8.35        82.39        65.85         9.93 
TCGA-NH-A8F8 TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 
       12.00        24.13        13.55        65.98        20.05        34.03 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N 
        1.02        19.99        36.03        15.95        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 
        1.94        38.96         6.05         4.73        13.97        11.01 
TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6702 
       10.98        30.05         0.49        16.31        28.57 

$`9Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       11.47         4.80        11.47        43.76        46.65        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       16.57        37.05        37.25        37.02        34.65        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-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-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-3514 
       37.05         1.02        35.01        58.03        63.98         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-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-3556 TCGA-AA-3558 
       21.01        13.02        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-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-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-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-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        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-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-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        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-6004 TCGA-AY-5543 TCGA-AY-6196 
       16.44         0.46         0.92        27.09        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        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 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        12.10       100.01        11.74         2.24         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         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        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        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        13.05        11.08        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       12.26        19.59        13.51        11.51        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        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        47.15        52.80 
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-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       13.05        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        9.70        30.28        70.03        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        12.72        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        10.39        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         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-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99         0.99         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-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         9.07         1.02        70.03        64.01 
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 
        0.49         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.05         6.97         9.37        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       36.00        12.95        13.05        10.06         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-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-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        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-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30         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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            85.05            140.38 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.99             19.07 
[1] "0.3 - 85.0 (20.0)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    51  22
  9Q LOSS WILD-TYPE 391 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     51   22
  9Q LOSS WILD-TYPE  391  140
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON               51               391
  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        15         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         18         69         47       47
                   vv
clus                STAGE IVA STAGE IVB
  9Q LOSS MUTATED           4         0
  9Q LOSS WILD-TYPE        23         2
D58V4, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               15               156
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                2                24
  STAGE IIIA               3                18
  STAGE IIIB              10                69
  STAGE IIIC               7                47
  STAGE IV                14                47
  STAGE IVA                4                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
  9Q LOSS MUTATED     3  17  43  12
  9Q LOSS WILD-TYPE  17  90 370  54
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               3                17
  T2              17                90
  T3              43               370
  T4              12                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 LOSS MUTATED    37  22  16
  9Q LOSS WILD-TYPE 305 127  98
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              37               305
  N1              22               127
  N2              16                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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    50  18
  9Q LOSS WILD-TYPE 398  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     50   18
  9Q LOSS WILD-TYPE  398   68
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              50               398
  1              18                68
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    32  43
  9Q LOSS WILD-TYPE 254 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     32   43
  9Q LOSS WILD-TYPE  254  279
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              32               254
  MALE                43               279
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                     49                             2
  9Q LOSS WILD-TYPE                  332                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                      21                              1
  9Q LOSS WILD-TYPE                   125                             12
D58V9, multiclass
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        49               332
  COLON MUCINOUS ADENOCARCINOMA                2                58
  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"
D58V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  74
  9Q LOSS WILD-TYPE   8 525
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   74
  9Q LOSS WILD-TYPE    8  525
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 8
  YES              74               525
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    49   2   8   3
  9Q LOSS WILD-TYPE 390   3  28  26
D58V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              49               390
  R1               2                 3
  R2               8                28
  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
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           7    39
  9Q LOSS WILD-TYPE                        53   253
D58V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      7                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"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    83  15
  10P LOSS WILD-TYPE 385 100
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                98                485 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                100 
$`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-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 
       16.44        14.50         0.20         5.65         5.13        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       62.79        29.56         3.19         3.29         0.26         1.35 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 
        8.02        29.06        22.03        15.02        15.02        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6898 
       13.02        15.02        11.08        11.08        17.75         7.53 
TCGA-D5-6926 TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 
        9.04        13.41        82.39        65.85        55.04        36.72 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 
       26.04        46.75        12.79        13.05        30.28        24.13 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3593 
       13.55        12.72        10.39        65.98        46.03        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         0.49         4.73        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 
       15.02        36.00        13.05        10.06       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 
        0.46        26.43 

$`10P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        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-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
TCGA-A6-6649 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-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        5.03         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         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-3553 
       12.99         0.99        14.01        33.99        21.01        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-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-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-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-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-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        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-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        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-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        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        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         4.21        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-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        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        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94        83.80        22.36        61.41        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         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        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        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
        5.03        17.03        15.02        12.00        14.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        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-D5-6532 
       19.59        13.51        11.51        20.19        20.42        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
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-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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        28.21         8.35        23.51        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        51.75        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2689 
       32.98         8.42        31.30         9.70        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        15.39        20.02        86.63        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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02         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-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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-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         0.99 
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-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-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         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-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 
       10.98        11.01        15.02        12.99        12.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        18.28        55.76        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               0.2                0.0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             140.38 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             17.39              19.07 
[1] "0.2 - 129.3 (17.4)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    66  33
  10P LOSS WILD-TYPE 376 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     66   33
  10P LOSS WILD-TYPE  376  129
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON                66                376
  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       151         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           3          6         14         11       13
  10P LOSS WILD-TYPE        23         15         65         43       48
                    vv
clus                 STAGE IVA STAGE IVB
  10P LOSS MUTATED           6         1
  10P LOSS WILD-TYPE        21         1
D59V4, 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                151
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                6                 15
  STAGE IIIB               14                 65
  STAGE IIIC               11                 43
  STAGE IV                 13                 48
  STAGE IVA                 6                 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
  10P LOSS MUTATED     2  20  67  11
  10P LOSS WILD-TYPE  18  87 346  55
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                2                 18
  T2               20                 87
  T3               67                346
  T4               11                 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
  10P LOSS MUTATED    47  30  23
  10P LOSS WILD-TYPE 295 119  91
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               47                295
  N1               30                119
  N2               23                 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"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    70  19
  10P LOSS WILD-TYPE 378  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     70   19
  10P LOSS WILD-TYPE  378   67
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               70                378
  1               19                 67
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46  54
  10P LOSS WILD-TYPE 240 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46   54
  10P LOSS WILD-TYPE  240  268
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               46                240
  MALE                 54                268
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                     60                             6
  10P LOSS WILD-TYPE                  321                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                      27                              6
  10P LOSS WILD-TYPE                   119                              7
D59V9, multiclass
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         60                321
  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"
D59V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     5  95
  10P LOSS WILD-TYPE   4 504
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   95
  10P LOSS WILD-TYPE    4  504
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 5                  4
  YES               95                504
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    75   0   6   5
  10P LOSS WILD-TYPE 364   5  30  24
D59V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               75                364
  R1                0                  5
  R2                6                 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"
D59V12, 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                        51   236
D59V13, 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                 51
  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"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    90  17
  10Q LOSS WILD-TYPE 378  98
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               107                476 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                17                 98 
$`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 
        0.26         1.35         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         7.53         9.04 
TCGA-D5-6929 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 
       13.41        33.67        55.04        36.72        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        13.05        30.28        24.13        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 
       12.72        10.39        65.98        32.02        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 
        6.05        29.98        36.95         1.02        19.99        13.94 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X TCGA-CI-6624 
       25.97        37.02        12.00        10.98        41.00         4.73 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF 
       13.97        36.00        13.05        10.06       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 
        0.49        17.00        16.34        16.31        16.41        11.97 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       28.57         0.66         0.46        47.08        26.43 

$`10Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        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-A6-5660 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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.06        27.09        24.13         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       20.28        16.24        24.92        61.84        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         3.02        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-3519 
       63.98         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-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-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
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-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-3851 TCGA-AA-3852 
       14.93         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        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-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-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        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-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         4.21        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-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        27.09         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        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 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        2.14         3.25         0.07         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.01        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        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         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-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        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        28.21         8.35        82.39        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        51.75        45.11 
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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       35.80        26.17        47.15        52.80        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        12.00        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         9.70        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       39.48        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       14.50        16.83        15.39        20.02        86.63        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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       24.00         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
       32.98         0.99         0.99        19.99         1.02        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       13.02        35.01        14.01        48.03        32.02        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         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        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-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       11.01        15.02        12.99        12.00        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95         5.29       126.44        41.36        57.24 
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-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        15.85        17.69         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19         0.69         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6235 
       18.28        55.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.26               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             140.38 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             22.03              19.04 
[1] "0.3 - 129.3 (22.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.3"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    72  37
  10Q LOSS WILD-TYPE 370 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     72   37
  10Q LOSS WILD-TYPE  370  125
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON                72                370
  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       144         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           3          6         14         14       13
  10Q LOSS WILD-TYPE        23         15         65         40       48
                    vv
clus                 STAGE IVA STAGE IVB
  10Q LOSS MUTATED           5         1
  10Q LOSS WILD-TYPE        22         1
D60V4, 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                144
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                6                 15
  STAGE IIIB               14                 65
  STAGE IIIC               14                 40
  STAGE IV                 13                 48
  STAGE IVA                 5                 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
  10Q LOSS MUTATED     3  20  75  11
  10Q LOSS WILD-TYPE  17  87 338  55
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                3                 17
  T2               20                 87
  T3               75                338
  T4               11                 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
  10Q LOSS MUTATED    55  29  25
  10Q LOSS WILD-TYPE 287 120  89
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               55                287
  N1               29                120
  N2               25                 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"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    81  18
  10Q LOSS WILD-TYPE 367  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     81   18
  10Q LOSS WILD-TYPE  367   68
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               81                367
  1               18                 68
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    50  60
  10Q LOSS WILD-TYPE 236 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     50   60
  10Q LOSS WILD-TYPE  236  262
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               50                236
  MALE                 60                262
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                     66                             6
  10Q LOSS WILD-TYPE                  315                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                      31                              6
  10Q LOSS WILD-TYPE                   115                              7
D60V9, multiclass
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         66                315
  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"
D60V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5 105
  10Q LOSS WILD-TYPE   4 494
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5  105
  10Q LOSS WILD-TYPE    4  494
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 5                  4
  YES              105                494
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    83   1   7   5
  10Q LOSS WILD-TYPE 356   4  29  24
D60V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               83                356
  R1                1                  4
  R2                7                 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"
D60V12, 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                        50   233
D60V13, 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                 50
  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"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    59  11
  11P LOSS WILD-TYPE 409 104
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                70                513 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                104 
$`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-6196 TCGA-AY-A69D 
       40.96         5.79        16.44        14.50         0.20        17.85 
TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5863 
        1.41         2.14         0.26        49.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 
       15.02        14.04        11.01        45.40        20.19        43.27 
TCGA-D5-6924 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC 
       14.30         7.50        36.72        36.00        18.18        12.79 
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 
       43.04        14.50        15.39        10.39        32.02         7.07 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 
        6.05        32.98         1.02        13.94        12.00        10.98 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 TCGA-DT-5265 
       41.00         0.49         0.69        13.97        15.02         5.29 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
       24.13        17.00        16.41         0.69 

$`11P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       34.65        14.53        32.91        31.63        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 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-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-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        61.02        78.08         6.97        54.02        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-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        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-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       27.02        29.98        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       26.01        24.00        20.98        34.03        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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        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-A71X TCGA-AY-A8YK 
       15.75        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        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-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       22.03        22.98        30.08        16.01        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-D5-5538 
       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        13.51        11.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         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-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-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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        39.42        35.93        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        47.15 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80        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-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30         9.70        30.28        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
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-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-A00Y TCGA-AG-A011 
        0.99        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.95        36.03         9.07         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-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         1.45         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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        36.00        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.06       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-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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.2                0.0 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             50.99             140.38 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            15.205             19.430 
[1] "0.2 - 51.0 (15.2)"  "0.0 - 140.4 (19.4)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  23
  11P LOSS WILD-TYPE 392 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   23
  11P LOSS WILD-TYPE  392  139
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON                50                392
  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       157        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         19         69         43       53
                    vv
clus                 STAGE IVA STAGE IVB
  11P LOSS MUTATED           5         1
  11P LOSS WILD-TYPE        22         1
D61V4, 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                157
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 5                 21
  STAGE IIIA                2                 19
  STAGE IIIB               10                 69
  STAGE IIIC               11                 43
  STAGE IV                  8                 53
  STAGE IVA                 5                 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
  11P LOSS MUTATED     2  14  46  12
  11P LOSS WILD-TYPE  18  93 367  54
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 18
  T2               14                 93
  T3               46                367
  T4               12                 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
  11P LOSS MUTATED    30  24  20
  11P LOSS WILD-TYPE 312 125  94
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               30                312
  N1               24                125
  N2               20                 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"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  13
  11P LOSS WILD-TYPE 398  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   13
  11P LOSS WILD-TYPE  398   73
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               50                398
  1               13                 73
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    34  40
  11P LOSS WILD-TYPE 252 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     34   40
  11P LOSS WILD-TYPE  252  282
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               34                252
  MALE                 40                282
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                     43                             7
  11P LOSS WILD-TYPE                  338                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                      18                              4
  11P LOSS WILD-TYPE                   128                              9
D61V9, multiclass
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         43                338
  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"
D61V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  72
  11P LOSS WILD-TYPE   7 527
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   72
  11P LOSS WILD-TYPE    7  527
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 2                  7
  YES               72                527
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    53   0   5   4
  11P LOSS WILD-TYPE 386   5  31  25
D61V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               53                386
  R1                0                  5
  R2                5                 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"
D61V12, 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                        56   257
D61V13, 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                 56
  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"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    69  17
  11Q LOSS WILD-TYPE 399  98
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                86                497 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                 98 
$`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-6196 TCGA-AY-A69D 
       22.42        16.44        14.50         0.95         0.20        17.85 
TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 
       19.33         1.41         2.14         0.26         2.01        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 
        5.03        15.02        15.02        14.04        11.01        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 
       45.40        20.19        43.27        17.85        14.30       130.65 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC 
       49.91         7.50        36.72        36.00        18.18        12.79 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       43.04        13.55        19.10        14.50        15.39        10.39 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3896 
       32.02         7.07         2.01         6.05        32.98         1.02 
TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       13.94        12.00        10.98         0.49         0.69        10.19 
TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF 
       13.97        13.97        10.98        30.05         5.29        24.13 
TCGA-EI-6509 TCGA-EI-6881 
       17.00        16.41 

$`11Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        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-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       13.94        37.05        37.25        37.02        34.65        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-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-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        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-3663 
       19.99        13.94        19.99        61.02        78.08         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-3696 
       15.02        11.01         5.98        37.05        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-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
        2.01        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        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        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        51.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       15.75        21.44        17.82        17.26        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       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-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.98        16.01        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       20.42        17.75        18.25         1.32        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         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20        92.75        13.32        12.59       140.38        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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        39.42        35.93        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        47.15 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80        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-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30         9.70        30.28        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       17.23        12.72        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-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98         1.02         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-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        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-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         1.45 
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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.73        78.12         7.17        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02        12.99        12.00        15.02        36.00        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       126.44        41.36        57.24       129.27 
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-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        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-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        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 
        0.46        18.28        55.76        47.08        26.43 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.2                0.0 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            130.65             140.38 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            16.425             19.960 
[1] "0.2 - 130.7 (16.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    61  27
  11Q LOSS WILD-TYPE 381 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     61   27
  11Q LOSS WILD-TYPE  381  135
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON                61                381
  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       150        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         18         66         44       49
                    vv
clus                 STAGE IVA STAGE IVB
  11Q LOSS MUTATED           4         1
  11Q LOSS WILD-TYPE        23         1
D62V4, 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                150
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 5                 21
  STAGE IIIA                3                 18
  STAGE IIIB               13                 66
  STAGE IIIC               10                 44
  STAGE IV                 12                 49
  STAGE IVA                 4                 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
  11Q LOSS MUTATED     4  16  60  12
  11Q LOSS WILD-TYPE  16  91 353  54
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 16
  T2               16                 91
  T3               60                353
  T4               12                 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
  11Q LOSS MUTATED    43  30  19
  11Q LOSS WILD-TYPE 299 119  95
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               43                299
  N1               30                119
  N2               19                 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
  11Q LOSS MUTATED    62  16
  11Q LOSS WILD-TYPE 386  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     62   16
  11Q LOSS WILD-TYPE  386   70
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               62                386
  1               16                 70
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    46  46
  11Q LOSS WILD-TYPE 240 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     46   46
  11Q LOSS WILD-TYPE  240  276
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               46                240
  MALE                 46                276
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                     53                             8
  11Q LOSS WILD-TYPE                  328                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                      21                              5
  11Q LOSS WILD-TYPE                   125                              8
D62V9, multiclass
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         53                328
  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"
D62V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  89
  11Q LOSS WILD-TYPE   6 510
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   89
  11Q LOSS WILD-TYPE    6  510
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                  6
  YES               89                510
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    65   0   6   4
  11Q LOSS WILD-TYPE 374   5  30  25
D62V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               65                374
  R1                0                  5
  R2                6                 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"
D62V12, 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                        55   244
D62V13, 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                 55
  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"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    48  18
  12P LOSS WILD-TYPE 420  97
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                66                517 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                 97 
$`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        14.04 
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        13.38        16.24        65.85 
TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-3913 
       36.72        36.00        13.05        30.28        43.04        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-A00Y 
       14.50        15.39        34.03        29.98        48.03        23.01 
TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG 
       70.03        10.19        13.97        10.98        24.13        51.48 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       20.91        17.00        16.31        16.41        28.57         0.66 

$`12P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 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-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         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-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        12.99         0.99        14.01 
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-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-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-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-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-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        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-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-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        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-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        22.36        62.79        61.41        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-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        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 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        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        51.75        45.11        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        47.15        52.80        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        12.00        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         9.70        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        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-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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        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         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        31.00        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         0.49         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81         6.05         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 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        15.02        36.00        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         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-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       37.51        31.30         0.39        32.19         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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.66               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             140.38 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            18.655             19.070 
[1] "0.7 - 70.0 (18.7)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.5"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    46  23
  12P LOSS WILD-TYPE 396 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     46   23
  12P LOSS WILD-TYPE  396  139
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON                46                396
  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       156         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         18         69         43       52
                    vv
clus                 STAGE IVA STAGE IVB
  12P LOSS MUTATED           5         0
  12P LOSS WILD-TYPE        22         2
D63V4, 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                156
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 2                 24
  STAGE IIIA                3                 18
  STAGE IIIB               10                 69
  STAGE IIIC               11                 43
  STAGE IV                  9                 52
  STAGE IVA                 5                 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
  12P LOSS MUTATED     3   9  54   4
  12P LOSS WILD-TYPE  17  98 359  62
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 17
  T2                9                 98
  T3               54                359
  T4                4                 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
  12P LOSS MUTATED    30  23  17
  12P LOSS WILD-TYPE 312 126  97
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               30                312
  N1               23                126
  N2               17                 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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    45  13
  12P LOSS WILD-TYPE 403  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     45   13
  12P LOSS WILD-TYPE  403   73
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               45                403
  1               13                 73
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    34  36
  12P LOSS WILD-TYPE 252 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     34   36
  12P LOSS WILD-TYPE  252  286
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               34                252
  MALE                 36                286
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                     45                             1
  12P LOSS WILD-TYPE                  336                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                      23                              0
  12P LOSS WILD-TYPE                   123                             13
D63V9, multiclass
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         45                336
  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"
D63V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  67
  12P LOSS WILD-TYPE   6 532
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   67
  12P LOSS WILD-TYPE    6  532
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                  6
  YES               67                532
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    54   0   4   2
  12P LOSS WILD-TYPE 385   5  32  27
D63V11, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               54                385
  R1                0                  5
  R2                4                 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"
D63V12, 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                        54   251
D63V13, 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                 54
  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"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    51  17
  12Q LOSS WILD-TYPE 417  98
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                68                515 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                17                 98 
$`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-AY-6196 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4750 
       14.50         0.20         2.14         0.26        49.08         8.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 
       29.06         5.03        14.04        29.03        15.02        11.01 
TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA 
       11.08         1.32        13.41        11.38        12.59         7.50 
TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-RU-A8FL 
       13.38        16.24        65.85        36.72        36.00        30.28 
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 
       43.04        14.50        15.39        34.03        29.98        48.03 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 
       23.01        15.95         0.49        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-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        33.53        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-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-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-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        29.00        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-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-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-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-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        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-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-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        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-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        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        75.25        50.37 
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        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 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-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-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-F4-6461 
       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 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        28.21         8.35        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        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        47.15        52.80 
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        13.05        12.00        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         9.70        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        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-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         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-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        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         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        37.02        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-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 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24       129.27        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         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        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39        32.19         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.2                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             65.85             140.38 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            17.015             19.100 
[1] "0.2 - 65.8 (17.0)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.5"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    48  21
  12Q LOSS WILD-TYPE 394 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     48   21
  12Q LOSS WILD-TYPE  394  141
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON                48                394
  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       157         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         17         70         43       52
                    vv
clus                 STAGE IVA STAGE IVB
  12Q LOSS MUTATED           5         0
  12Q LOSS WILD-TYPE        22         2
D64V4, 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                157
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 1                 25
  STAGE IIIA                4                 17
  STAGE IIIB                9                 70
  STAGE IIIC               11                 43
  STAGE IV                  9                 52
  STAGE IVA                 5                 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
  12Q LOSS MUTATED     3  11  52   4
  12Q LOSS WILD-TYPE  17  96 361  62
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 17
  T2               11                 96
  T3               52                361
  T4                4                 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
  12Q LOSS MUTATED    29  23  18
  12Q LOSS WILD-TYPE 313 126  96
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               29                313
  N1               23                126
  N2               18                 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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    44  14
  12Q LOSS WILD-TYPE 404  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     44   14
  12Q LOSS WILD-TYPE  404   72
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               44                404
  1               14                 72
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    32  38
  12Q LOSS WILD-TYPE 254 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     32   38
  12Q LOSS WILD-TYPE  254  284
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               32                254
  MALE                 38                284
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                     46                             2
  12Q LOSS WILD-TYPE                  335                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                      21                              0
  12Q LOSS WILD-TYPE                   125                             13
D64V9, multiclass
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         46                335
  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"
D64V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  68
  12Q LOSS WILD-TYPE   7 531
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   68
  12Q LOSS WILD-TYPE    7  531
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 2                  7
  YES               68                531
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    52   0   4   3
  12Q LOSS WILD-TYPE 387   5  32  26
D64V11, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               52                387
  R1                0                  5
  R2                4                 32
  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"
D64V12, 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                        56   247
D64V13, 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                 56
  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"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   4
  13Q LOSS WILD-TYPE 455 111
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                566 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                111 
$`13Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-A01D TCGA-AY-6196 TCGA-AZ-4681 
       23.01        18.05        24.00        10.98         0.20        83.80 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-F4-6704 TCGA-G4-6314 TCGA-QG-A5Z1 TCGA-AG-3594 
        3.19         3.29         1.55        35.93         8.42         2.01 
TCGA-AG-3600 TCGA-AG-A00Y TCGA-AG-A020 TCGA-DC-6156 TCGA-DY-A0XA 
        6.05        23.01        10.98        15.02       126.44 

$`13Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-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-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-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        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-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-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       27.02        29.98        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-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        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        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         4.21        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 
       15.75        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        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        61.41 
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         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25         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 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        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        35.41        19.43       107.67 
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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        36.72        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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80        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        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       32.98        31.30         9.70        30.28        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        12.72 
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-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
       12.00        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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.00        13.97        36.00        10.98        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06         5.29        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        37.51 
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         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.0 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             140.38 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            10.980             19.215 
[1] "0.2 - 126.4 (11.0)" "0.0 - 140.4 (19.2)"
[1] "hr=" "1.3"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    12   8
  13Q LOSS WILD-TYPE 430 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    8
  13Q LOSS WILD-TYPE  430  154
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON                12                430
  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       165        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         21         78         50       58
                    vv
clus                 STAGE IVA STAGE IVB
  13Q LOSS MUTATED           2         0
  13Q LOSS WILD-TYPE        25         2
D65V4, 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                165
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                0                 21
  STAGE IIIB                1                 78
  STAGE IIIC                4                 50
  STAGE IV                  3                 58
  STAGE IVA                 2                 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
  13Q LOSS MUTATED     1   2  14   3
  13Q LOSS WILD-TYPE  19 105 399  63
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                1                 19
  T2                2                105
  T3               14                399
  T4                3                 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
  13Q LOSS MUTATED     9   3   8
  13Q LOSS WILD-TYPE 333 146 106
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                9                333
  N1                3                146
  N2                8                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"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11   5
  13Q LOSS WILD-TYPE 437  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11    5
  13Q LOSS WILD-TYPE  437   81
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               11                437
  1                5                 81
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  11
  13Q LOSS WILD-TYPE 277 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE  277  311
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                277
  MALE                 11                311
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                      8                             3
  13Q LOSS WILD-TYPE                  373                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                       6                              2
  13Q LOSS WILD-TYPE                   140                             11
D65V9, multiclass
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          8                373
  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"
D65V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  20
  13Q LOSS WILD-TYPE   9 579
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   20
  13Q LOSS WILD-TYPE    9  579
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  9
  YES               20                579
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    16   0   1   1
  13Q LOSS WILD-TYPE 423   5  35  28
D65V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               16                423
  R1                0                  5
  R2                1                 35
  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"
D65V12, 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                        59   285
D65V13, 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                 59
  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"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   156  35
  14Q LOSS WILD-TYPE 312  80
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               191                392 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                 80 
$`14Q LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
        4.80        43.76        42.28        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       36.53        14.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13        25.08        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 
       23.87        20.28        61.84         5.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
        9.07        24.03        19.07        34.03        13.02        23.01 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       13.94        19.99         2.01        14.01        50.04        47.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 
       37.05        19.00        85.05        10.06        25.02        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 
       37.02        17.03        31.07        17.03        24.03        18.05 
TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       12.99        34.03        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       26.01        24.00         7.96        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       14.99        21.99        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 
       26.01         2.96         2.01        40.96         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D 
       27.42        16.44        14.50         0.95        15.75        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
       18.84        75.25         1.41         5.65        22.36        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
        5.23         1.94         3.06         2.14         0.07         0.26 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 
       49.08         2.01        25.02         8.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       29.03        13.02        15.02        11.08        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       12.26        13.51        18.25         1.32        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A288 
       13.41        11.38        38.20        13.32       140.38        14.04 
TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
      119.93        13.38        29.59        33.67        13.25         0.53 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T 
       28.21         8.35        82.39        36.72        91.79        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 
       19.33        15.65        13.05        12.00        30.28        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N 
       17.23        13.55        37.74        10.39        65.98        11.84 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 
       36.03        46.03        34.03        50.04         6.05         0.99 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        0.99         1.02        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         0.49        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         9.37         4.73        13.97         7.17        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97        36.00        10.98        13.05        10.06 
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-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       24.33        44.91        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       37.02        31.63        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        29.16        27.09         8.38        25.18        24.16 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        56.25 
TCGA-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-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       37.05        36.03         8.05        19.07         0.00        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-3558 TCGA-AA-3560 
       21.01        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.05        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       26.99        19.04        19.04        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        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-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        29.98        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-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
        2.01        13.05        25.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C 
       18.05         4.01         0.99        17.03        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        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-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 
        0.20        21.44        17.82        17.26        19.33        50.37 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       58.39        32.94         5.13        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.19         2.24         3.25         3.29         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.08        11.01        12.03        19.59        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        26.47        81.37        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        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       35.41        19.43       107.67        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.00        26.43        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        47.15        52.80 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98        19.33         9.93        12.79        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30         9.70        70.03        24.13 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        12.72        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        86.63        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
        8.02         7.07        20.05        24.00         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       29.98         1.02        32.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 
       13.02        14.01        32.02        19.99        28.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98        13.94        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-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98        49.97        61.97        41.00         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72        26.43         1.81         6.97        78.12 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       10.98        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       17.69         8.61        11.51        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        9.96        37.51        28.57         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6572 
        0.46        47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            140.38             139.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            18.050             19.625 
[1] "0.1 - 140.4 (18.1)" "0.0 - 139.2 (19.6)"
[1] "hr=" "1"  
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   134  66
  14Q LOSS WILD-TYPE 308  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    134   66
  14Q LOSS WILD-TYPE  308   96
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON               134                308
  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        58         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         12         51         39       35
                    vv
clus                 STAGE IVA STAGE IVB
  14Q LOSS MUTATED          12         0
  14Q LOSS WILD-TYPE        15         2
D66V4, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  30                 74
  STAGE IA                  0                  1
  STAGE II                  8                 28
  STAGE IIA                58                113
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                10                 16
  STAGE IIIA                9                 12
  STAGE IIIB               28                 51
  STAGE IIIC               15                 39
  STAGE IV                 26                 35
  STAGE IVA                12                 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
  14Q LOSS MUTATED     9  31 143  19
  14Q LOSS WILD-TYPE  11  76 270  47
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                9                 11
  T2               31                 76
  T3              143                270
  T4               19                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  14Q LOSS MUTATED   103  63  36
  14Q LOSS WILD-TYPE 239  86  78
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              103                239
  N1               63                 86
  N2               36                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   143  38
  14Q LOSS WILD-TYPE 305  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    143   38
  14Q LOSS WILD-TYPE  305   48
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              143                305
  1               38                 48
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    91 111
  14Q LOSS WILD-TYPE 195 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     91  111
  14Q LOSS WILD-TYPE  195  211
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               91                195
  MALE                111                211
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                    129                             4
  14Q LOSS WILD-TYPE                  252                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                      64                              1
  14Q LOSS WILD-TYPE                    82                             12
D66V9, multiclass
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        129                252
  COLON MUCINOUS ADENOCARCINOMA                 4                 56
  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"
D66V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     3 199
  14Q LOSS WILD-TYPE   6 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  199
  14Q LOSS WILD-TYPE    6  400
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 3                  6
  YES              199                400
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   141   2  12  10
  14Q LOSS WILD-TYPE 298   3  24  19
D66V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              141                298
  R1                2                  3
  R2               12                 24
  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"
D66V12, 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                          20    96
  14Q LOSS WILD-TYPE                        40   196
D66V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      20                 40
  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"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   175  39
  15Q LOSS WILD-TYPE 293  76
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               214                369 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                39                 76 
$`15Q LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        4.80        43.76        43.76        43.43        24.33        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       45.60        16.57        34.65        36.53        32.45        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       29.19        29.16        22.52        25.08        20.61        21.76 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       20.28        61.84         5.03         7.04         1.02         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
        9.07        37.05        29.00        12.99        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 
       13.02        23.01        19.99        19.99         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 
       37.05        19.00        36.00        85.05        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        36.03         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       17.03        24.03        29.98        12.99         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D 
       50.99        13.05        34.06        24.00        27.02        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 
       31.00        33.04        26.01         2.96        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        27.42        14.50        16.31         0.95        15.75 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       17.85        18.84        83.80        65.00        62.79        61.41 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 
       29.56         5.23         3.19         2.14         0.26         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
      102.44        49.08         2.01        25.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       16.04        15.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       12.03        20.19         1.32        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       92.75        13.32        12.59       140.38       131.51         6.12 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
       95.18        13.38        35.87         1.55        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 
       13.25         0.53        35.41         8.35        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       45.11        36.72        36.00        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       19.33        12.79        29.46         9.70        30.28        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L 
       43.04        13.55        37.74        14.50        10.39        65.98 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
       32.02        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 
        6.05        19.99        29.98         0.99        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       35.01         1.02        19.99        28.04        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
       13.94        25.97        23.01        37.02         1.02        12.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        1.94        38.96        41.00        38.04         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 
       10.19         6.05         9.37         7.17        10.98        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.97        36.00        13.05        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
        0.49         2.40        15.85        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       10.78        13.64        11.97        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69        18.28        26.43 

$`15Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       11.47        11.47        46.65        42.90        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       13.94        37.05        37.25        37.02        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       27.09        24.13         8.38        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       56.25         9.63         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 
       34.03        29.00        26.01         0.99        14.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-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-3844 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       33.07         0.00        32.05        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 
       24.00         2.01        20.98        34.03        16.08        26.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
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-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
        0.99        21.99        34.98        10.98        32.02        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-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        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-6964 
       21.37         4.21        56.55         0.79         0.72        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
        0.20        16.44         0.46         0.92        27.09         0.20 
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        75.25        50.37 
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         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       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 
       16.01        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        13.51        11.51 
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        12.39        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        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       13.45         6.18        16.31        29.59        19.43       107.67 
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        51.75        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        47.15        52.80 
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        13.05        12.00 
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        12.72        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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        7.07         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 
        0.99         1.02        36.95        13.02        14.01        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       32.02        36.03         1.02         0.99        20.98         6.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       26.43         1.81         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       78.12        11.01        15.02        12.00        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       30.05        12.95        10.06         5.29       126.44       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       18.28        17.69        16.34         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        9.96        37.51         0.39         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.26               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            140.38             139.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.99              19.04 
[1] "0.3 - 140.4 (20.0)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   152  70
  15Q LOSS WILD-TYPE 290  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    152   70
  15Q LOSS WILD-TYPE  290   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON               152                290
  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        57         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           7         11         30         26       31
  15Q LOSS WILD-TYPE        19         10         49         28       30
                    vv
clus                 STAGE IVA STAGE IVB
  15Q LOSS MUTATED          12         1
  15Q LOSS WILD-TYPE        15         1
D67V4, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  33                 71
  STAGE IA                  0                  1
  STAGE II                  7                 29
  STAGE IIA                57                114
  STAGE IIB                 3                  7
  STAGE IIC                 2                  1
  STAGE III                 7                 19
  STAGE IIIA               11                 10
  STAGE IIIB               30                 49
  STAGE IIIC               26                 28
  STAGE IV                 31                 30
  STAGE IVA                12                 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
  15Q LOSS MUTATED     9  32 161  23
  15Q LOSS WILD-TYPE  11  75 252  43
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                 11
  T2               32                 75
  T3              161                252
  T4               23                 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
  15Q LOSS MUTATED   109  66  50
  15Q LOSS WILD-TYPE 233  83  64
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              109                233
  N1               66                 83
  N2               50                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   155  43
  15Q LOSS WILD-TYPE 293  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    155   43
  15Q LOSS WILD-TYPE  293   43
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              155                293
  1               43                 43
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   101 124
  15Q LOSS WILD-TYPE 185 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    101  124
  15Q LOSS WILD-TYPE  185  198
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              101                185
  MALE                124                198
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                    139                            12
  15Q LOSS WILD-TYPE                  242                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                      64                              5
  15Q LOSS WILD-TYPE                    82                              8
D67V9, multiclass
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        139                242
  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"
D67V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7 218
  15Q LOSS WILD-TYPE   2 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7  218
  15Q LOSS WILD-TYPE    2  381
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                  2
  YES              218                381
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   160   2  15   9
  15Q LOSS WILD-TYPE 279   3  21  20
D67V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              160                279
  R1                2                  3
  R2               15                 21
  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"
D67V12, 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                          18   115
  15Q LOSS WILD-TYPE                        42   177
D67V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      18                 42
  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"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    28   9
  16P LOSS WILD-TYPE 440 106
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                546 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                106 
$`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-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 
       16.31         0.20        17.85         5.65         3.19        22.03 
TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       15.02        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL TCGA-AG-3578 
       49.91         7.50        18.18        10.98        30.28        32.02 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-4005 TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 
        6.05        19.99        14.04        13.05        32.19         0.53 
TCGA-G5-6233 
       18.28 

$`16P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        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-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-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        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-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        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-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-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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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-6890 
       40.96         0.07        21.37         4.21        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-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        15.75        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        75.25        50.37        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        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        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         1.94         2.24         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         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        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        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        15.02        14.04        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-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        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         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
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        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        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-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80        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        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30         9.70        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        12.72 
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-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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
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-4007 TCGA-AG-4008 
       32.02        19.99        28.04        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        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         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         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 
       37.51        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         0.46        55.76        47.08        26.43 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               0.2                0.0 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             61.84             140.38 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             16.44              19.33 
[1] "0.2 - 61.8 (16.4)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1.7"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    30  10
  16P LOSS WILD-TYPE 412 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     30   10
  16P LOSS WILD-TYPE  412  152
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON                30                412
  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        16         0         1
  16P LOSS WILD-TYPE     101        1       35       155        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         21         73         48       58
                    vv
clus                 STAGE IVA STAGE IVB
  16P LOSS MUTATED           4         0
  16P LOSS WILD-TYPE        23         2
D68V4, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                16                155
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 0                 26
  STAGE IIIA                0                 21
  STAGE IIIB                6                 73
  STAGE IIIC                6                 48
  STAGE IV                  3                 58
  STAGE IVA                 4                 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
  16P LOSS MUTATED     0   4  31   5
  16P LOSS WILD-TYPE  20 103 382  61
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                 20
  T2                4                103
  T3               31                382
  T4                5                 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
  16P LOSS MUTATED    21   8  11
  16P LOSS WILD-TYPE 321 141 103
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               21                321
  N1                8                141
  N2               11                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"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    27   7
  16P LOSS WILD-TYPE 421  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     27    7
  16P LOSS WILD-TYPE  421   79
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               27                421
  1                7                 79
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    21  19
  16P LOSS WILD-TYPE 265 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     21   19
  16P LOSS WILD-TYPE  265  303
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               21                265
  MALE                 19                303
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                     24                             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
D68V9, multiclass
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         24                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"
D68V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  40
  16P LOSS WILD-TYPE   9 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   40
  16P LOSS WILD-TYPE    9  559
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  9
  YES               40                559
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    29   1   0   1
  16P LOSS WILD-TYPE 410   4  36  28
D68V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               29                410
  R1                1                  4
  R2                0                 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"
D68V12, 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                           8    21
  16P LOSS WILD-TYPE                        52   271
D68V13, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       8                 52
  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"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    32   7
  16Q LOSS WILD-TYPE 436 108
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                39                544 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                108 
$`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-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 TCGA-CM-5863 
        0.20        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-A1DA 
       13.02        11.01        11.01        20.19        17.75         7.50 
TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3600 
       18.18        10.98        30.28        10.39        32.02         6.05 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-4005 TCGA-DC-6682 
       19.99         7.99        32.98         1.02        14.04        13.05 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
       32.19         0.53        18.28 

$`16Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        5.03         7.04         3.02        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-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-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-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-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        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-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        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-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        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        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         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        5.79        22.42        27.42        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        15.75        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        75.25        50.37 
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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        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         1.94         2.24 
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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
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        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        15.02        14.04        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        13.51        11.51        20.42        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        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-A280 TCGA-DM-A282 
      140.38        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        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        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 
       35.41        19.43       107.67        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        51.75        45.11        39.42        35.93        36.72 
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-A50V 
       26.17        91.79        46.75        47.15        52.80        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        13.05        12.00 
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         9.70 
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        12.72        37.74        10.39        14.50        16.83 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        19.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03         1.02        17.03         0.99        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         0.49         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         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00        10.98        30.05        12.95        10.06 
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-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-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       28.57         0.39         0.66         0.69         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.0 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             41.00             140.38 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.31              19.38 
[1] "0.2 - 41.0 (16.3)"  "0.0 - 140.4 (19.4)"
[1] "hr=" "1.4"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    28  14
  16Q LOSS WILD-TYPE 414 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     28   14
  16Q LOSS WILD-TYPE  414  148
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON                28                414
  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        14         0         1
  16Q LOSS WILD-TYPE      98        1       35       157        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         21         73         47       57
                    vv
clus                 STAGE IVA STAGE IVB
  16Q LOSS MUTATED           3         0
  16Q LOSS WILD-TYPE        24         2
D69V4, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   6                 98
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                14                157
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 0                 26
  STAGE IIIA                0                 21
  STAGE IIIB                6                 73
  STAGE IIIC                7                 47
  STAGE IV                  4                 57
  STAGE IVA                 3                 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
  16Q LOSS MUTATED     0   7  30   5
  16Q LOSS WILD-TYPE  20 100 383  61
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                 20
  T2                7                100
  T3               30                383
  T4                5                 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
  16Q LOSS MUTATED    23   7  12
  16Q LOSS WILD-TYPE 319 142 102
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               23                319
  N1                7                142
  N2               12                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"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    29   6
  16Q LOSS WILD-TYPE 419  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     29    6
  16Q LOSS WILD-TYPE  419   80
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               29                419
  1                6                 80
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  21
  16Q LOSS WILD-TYPE 265 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   21
  16Q LOSS WILD-TYPE  265  301
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                265
  MALE                 21                301
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                     23                             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
D69V9, multiclass
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         23                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"
D69V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  41
  16Q LOSS WILD-TYPE   8 558
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   41
  16Q LOSS WILD-TYPE    8  558
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  8
  YES               41                558
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    30   1   1   1
  16Q LOSS WILD-TYPE 409   4  35  28
D69V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               30                409
  R1                1                  4
  R2                1                 35
  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
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           8    19
  16Q LOSS WILD-TYPE                        52   273
D69V13, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 12
  BLACK OR AFRICAN AMERICAN                       8                 52
  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"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   251  68
  17P LOSS WILD-TYPE 217  47
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               319                264 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                68                 47 
$`17P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.76        43.43        24.33        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        31.63        30.44        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6654 
       22.52        24.13        25.18        24.16        20.61        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       20.28        61.84         5.03         7.04         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02         6.97        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       36.03        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       10.06        25.02        38.99        36.95        37.02        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       33.07        32.05         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3952 
       27.02        29.98        18.05         2.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       20.98        34.03        16.08        50.99        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
       27.02         7.96        19.00        34.03        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D 
       42.02        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       32.02        12.00         1.02        33.04        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6548 
       39.98         2.01         5.03        41.00        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         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        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 
        0.20        17.85        75.25         1.41         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
       83.80        22.36        65.00        61.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
        5.23         3.19         1.94         2.24         2.14         3.29 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        0.26         1.35        49.08        21.99         2.01        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
        8.02        27.02        13.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       17.03        29.03        21.99        14.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        13.05        11.08        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        17.13        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43        14.30         9.04        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 TCGA-F4-6807 
       35.97       117.07        13.38        11.11        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 
       33.67        13.25         8.35        23.51        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       55.04        45.11        39.42        35.93        36.72        26.43 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB 
       91.79        46.75        10.98        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        13.05        12.00        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        9.70        30.28        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        12.72        37.74        14.50        15.39        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        65.98        11.84        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       36.03        24.00        34.03         2.01        50.04         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 
        7.99         0.99         1.02        32.98         0.99         1.02 
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-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 
       70.03        64.01        51.98         1.94        41.00         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72        10.19         6.05         6.05         6.97 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       13.97         7.17        11.01        13.97        10.98        30.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       24.13        51.48         0.49         2.40        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       18.28        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39         0.69         0.53         0.76         0.46 
TCGA-G5-6235 
       55.76 

$`17P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 
       11.47         4.80        11.47        46.65        42.90        44.91 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5661 
       45.60        13.94        37.02        36.53        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 
       23.61        22.09        22.06         8.38        25.08        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       56.25         9.63         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02        13.02         1.02         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 
       19.07        34.03        29.00        26.01         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       29.95        20.98         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02        11.01         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 
       35.05         0.99         1.02        17.98        15.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3860 
        0.00        17.03         0.00         0.00        36.03        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00        12.99        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 
        2.01        21.99        13.05        34.06        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-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01K 
        4.01         0.99        34.98        15.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       38.07         1.02        35.01        35.01        26.01        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-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       56.55         0.72        10.88         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       32.94        62.79        49.41         6.77       100.01        11.74 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.06         3.25         0.07         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.93       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 
       15.02        12.00        14.04        16.04        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        12.03        20.19        20.42 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       15.12        17.85         4.80        16.14        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41         1.51        12.00        10.26       119.70 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G 
       49.91         7.50       135.65         7.76        81.37        60.79 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18         8.61        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       35.87         1.55        29.59         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21        82.39        74.56        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       51.75        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5YW 
       26.17        47.15        52.80        18.18        19.33        29.46 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 
       31.30        70.03        24.13        10.39        16.83        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       36.03         8.02        20.05         1.02        46.03        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 
        6.05        15.95        19.99        19.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 
       19.99        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
        0.99        20.98        36.03         9.07        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        38.04         1.45        26.43         1.81 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37         4.73        78.12        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1H8 
       12.00        15.02        36.00        12.95        13.05        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       20.55        19.96        15.85         8.61        13.64        17.46 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       32.19         0.66         1.12        18.28        47.08        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            140.38             135.65 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             18.28              19.33 
[1] "0.2 - 140.4 (18.3)" "0.0 - 135.7 (19.3)"
[1] "hr=" "1.2"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   229 102
  17P LOSS WILD-TYPE 213  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    229  102
  17P LOSS WILD-TYPE  213   60
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON               229                213
  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        84         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         15         45         37       43
  17P LOSS WILD-TYPE        12          6         34         17       18
                    vv
clus                 STAGE IVA STAGE IVB
  17P LOSS MUTATED          18         2
  17P LOSS WILD-TYPE         9         0
D70V4, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  46                 58
  STAGE IA                  0                  1
  STAGE II                 18                 18
  STAGE IIA                84                 87
  STAGE IIB                 3                  7
  STAGE IIC                 2                  1
  STAGE III                14                 12
  STAGE IIIA               15                  6
  STAGE IIIB               45                 34
  STAGE IIIC               37                 17
  STAGE IV                 43                 18
  STAGE IVA                18                  9
  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  54 233  39
  17P LOSS WILD-TYPE  11  53 180  27
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                9                 11
  T2               54                 53
  T3              233                180
  T4               39                 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"
                    vv
clus                  N0  N1  N2
  17P LOSS MUTATED   166  93  74
  17P LOSS WILD-TYPE 176  56  40
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              166                176
  N1               93                 56
  N2               74                 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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   236  61
  17P LOSS WILD-TYPE 212  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    236   61
  17P LOSS WILD-TYPE  212   25
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              236                212
  1               61                 25
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   150 185
  17P LOSS WILD-TYPE 136 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    150  185
  17P LOSS WILD-TYPE  136  137
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              150                136
  MALE                185                137
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                    213                            15
  17P LOSS WILD-TYPE                  168                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                      95                              6
  17P LOSS WILD-TYPE                    51                              7
D70V9, multiclass
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        213                168
  COLON MUCINOUS ADENOCARCINOMA                15                 45
  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"
D70V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7 328
  17P LOSS WILD-TYPE   2 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7  328
  17P LOSS WILD-TYPE    2  271
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 7                  2
  YES              328                271
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   234   3  25  11
  17P LOSS WILD-TYPE 205   2  11  18
D70V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              234                205
  R1                3                  2
  R2               25                 11
  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"
D70V12, 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                          30   165
  17P LOSS WILD-TYPE                        30   127
D70V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      30                 30
  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"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    71  22
  17Q LOSS WILD-TYPE 397  93
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                490 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                 93 
$`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-6196 
       41.00         5.79        22.42         0.20        14.50         0.20 
TCGA-AY-A69D TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4751 
       17.85        12.10         3.29         0.26        49.08        27.02 
TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-5864 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 
       13.02         5.03        15.02        45.40        43.27        12.49 
TCGA-D5-6924 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 
       14.30        11.38        38.20        12.59       140.38        13.38 
TCGA-F4-6704 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6314 TCGA-G4-6320 TCGA-NH-A50U 
        1.55        13.25         8.35        35.93        26.43        10.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QL-A97D 
       15.65        12.79        13.05        42.77        32.98         9.70 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3896 TCGA-AG-3902 
       14.50        15.39        65.98        36.03         1.02        32.02 
TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A02X 
       28.04        13.94        25.97        12.00        51.98        41.00 
TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF 
       10.19        13.97        10.98        10.06         5.29        24.13 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 
        0.49         2.40        17.69        16.41        11.51        28.57 
TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 
        0.53         0.76        55.76 

$`17Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        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-A6-5656 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-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02         1.02         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-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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        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-3663 
       20.98        13.94        19.99        61.02        78.08         6.97 
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-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-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-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-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-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        24.00        19.07        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-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-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         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         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72        27.42        10.88        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        15.75 
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        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        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 
       83.80        22.36        65.00        62.79        61.41        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-6715 
        1.94         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        13.51        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32         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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        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        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        36.72        36.00        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        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YW 
       18.18        19.33        19.33         9.93        12.00        29.46 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        30.28        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        12.72        37.74 
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-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03         0.99        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         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         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        13.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 
       18.28        15.85        16.34        16.31         8.61        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        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       31.30         0.39        32.19         0.66         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        47.08        26.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            140.38             139.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            17.690             19.085 
[1] "0.2 - 140.4 (17.7)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.4"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    67  28
  17Q LOSS WILD-TYPE 375 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     67   28
  17Q LOSS WILD-TYPE  375  134
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON                67                375
  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       153         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         16         65         41       50
                    vv
clus                 STAGE IVA STAGE IVB
  17Q LOSS MUTATED           6         1
  17Q LOSS WILD-TYPE        21         1
D71V4, 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                153
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 4                 22
  STAGE IIIA                5                 16
  STAGE IIIB               14                 65
  STAGE IIIC               13                 41
  STAGE IV                 11                 50
  STAGE IVA                 6                 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
  17Q LOSS MUTATED     0  16  65  15
  17Q LOSS WILD-TYPE  20  91 348  51
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                 20
  T2               16                 91
  T3               65                348
  T4               15                 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
  17Q LOSS MUTATED    41  32  23
  17Q LOSS WILD-TYPE 301 117  91
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               41                301
  N1               32                117
  N2               23                 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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    60  17
  17Q LOSS WILD-TYPE 388  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     60   17
  17Q LOSS WILD-TYPE  388   69
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               60                388
  1               17                 69
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    42  54
  17Q LOSS WILD-TYPE 244 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     42   54
  17Q LOSS WILD-TYPE  244  268
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               42                244
  MALE                 54                268
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                     58                             9
  17Q LOSS WILD-TYPE                  323                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                      26                              2
  17Q LOSS WILD-TYPE                   120                             11
D71V9, multiclass
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         58                323
  COLON MUCINOUS ADENOCARCINOMA                 9                 51
  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"
D71V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  94
  17Q LOSS WILD-TYPE   7 505
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   94
  17Q LOSS WILD-TYPE    7  505
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  7
  YES               94                505
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    68   1   7   6
  17Q LOSS WILD-TYPE 371   4  29  23
D71V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               68                371
  R1                1                  4
  R2                7                 29
  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"
D71V12, 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                        49   247
D71V13, 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                 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"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   293  66
  18P LOSS WILD-TYPE 175  49
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               359                224 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                66                 49 
$`18P LOSS MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       32.71        29.16        27.09        24.13        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 
        6.97        38.99         9.07        37.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01        15.02        37.05        19.00        36.00        85.05 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       10.06        33.07         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98        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-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-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        38.04        27.02        42.02        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        15.02        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       26.01         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
        0.20        16.44        14.50         0.95        15.75        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 
       17.85        18.84        75.25         5.65         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        65.00        62.79        12.10        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.94         2.24         2.14         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
        1.35        49.08        21.99         2.01        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.01        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 
        1.32        17.85        17.13        12.49         7.53        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        11.11        13.45 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
        0.53        35.41        28.21         8.35        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       65.85        55.04        45.11        35.93        36.72        36.00 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-NH-A8F7 
       46.75        47.15        18.18        10.98        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       12.00        42.77        32.98         8.42         9.70        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        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       37.74        10.39        14.50        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03        12.00         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 
       20.05        24.00        46.03        34.03        50.04         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
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-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        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-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X 
       31.00        70.03        10.98        51.98         1.94        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       38.04         0.49         0.69         0.72        26.43        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       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-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-F5-6465 
       16.41        11.51        10.78        13.64        11.97        37.51 
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-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        26.43 

$`18P LOSS WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 
       46.65        42.90        37.02        31.63        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 
       22.52         8.38        25.08        24.16        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-3520 TCGA-AA-3524 
       63.98         1.02        13.02         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
        8.05         0.00        29.00         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       29.95        20.98         6.97        54.02         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        0.00         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
        2.01        25.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       30.02        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       34.98        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O 
       35.01        35.01        37.02        39.06        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.72        10.88         0.46         0.92        27.09        16.31 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
        0.20        21.44        17.82        19.33        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        1.41        32.94        61.41        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         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        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         2.93       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        16.01        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        12.39        10.13 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         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        13.64         6.18        35.87        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        67.30        53.62        44.68        51.75 
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        52.80        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-3892 TCGA-AG-3894 
        6.05        19.99         0.99         0.99        13.02        14.01 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02G 
       14.04        20.98        36.03        64.01        49.97        38.96 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6814 
       20.91         8.61        17.46         8.45         9.96         0.53 
TCGA-F5-6861 TCGA-G5-6572 
        1.12        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.38             135.65 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            19.000             19.215 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.2)"
[1] "hr=" "1.1"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   245 126
  18P LOSS WILD-TYPE 197  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    245  126
  18P LOSS WILD-TYPE  197   36
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON               245                197
  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        97         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         14         54         37       49
  18P LOSS WILD-TYPE        15          7         25         17       12
                    vv
clus                 STAGE IVA STAGE IVB
  18P LOSS MUTATED          23         1
  18P LOSS WILD-TYPE         4         1
D72V4, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  57                 47
  STAGE IA                  0                  1
  STAGE II                 16                 20
  STAGE IIA                97                 74
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                11                 15
  STAGE IIIA               14                  7
  STAGE IIIB               54                 25
  STAGE IIIC               37                 17
  STAGE IV                 49                 12
  STAGE IVA                23                  4
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    12  62 259  41
  18P LOSS WILD-TYPE   8  45 154  25
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               12                  8
  T2               62                 45
  T3              259                154
  T4               41                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18P LOSS MUTATED   190 104  78
  18P LOSS WILD-TYPE 152  45  36
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              190                152
  N1              104                 45
  N2               78                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   261  72
  18P LOSS WILD-TYPE 187  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    261   72
  18P LOSS WILD-TYPE  187   14
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              261                187
  1               72                 14
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   172 202
  18P LOSS WILD-TYPE 114 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    172  202
  18P LOSS WILD-TYPE  114  120
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              172                114
  MALE                202                120
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                    232                            12
  18P LOSS WILD-TYPE                  149                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                     119                              7
  18P LOSS WILD-TYPE                    27                              6
D72V9, multiclass
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        232                149
  COLON MUCINOUS ADENOCARCINOMA                12                 48
  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"
D72V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     8 366
  18P LOSS WILD-TYPE   1 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8  366
  18P LOSS WILD-TYPE    1  233
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 8                  1
  YES              366                233
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   266   2  29  14
  18P LOSS WILD-TYPE 173   3   7  15
D72V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              266                173
  R1                2                  3
  R2               29                  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"
D72V12, 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                          37   184
  18P LOSS WILD-TYPE                        23   108
D72V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      37                 23
  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"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   313  75
  18Q LOSS WILD-TYPE 155  40
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               388                195 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                75                 40 
$`18Q LOSS MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       16.57        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-A6-5662 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-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02         6.97        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       36.03        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       12.99        14.01        33.99        13.02        24.00        23.01 
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-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       18.05        12.99        24.00         2.01        20.98        34.03 
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-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       24.00        27.02         7.96        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       32.02        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
        2.96        39.98         2.01         5.03        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         5.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L 
       16.44         0.46        14.50        16.31        15.75        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 
       17.85        18.84        75.25         5.65         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        61.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        5.23         1.94         2.24         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.26         1.35       102.44        49.08        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       16.04        21.99        13.02        15.02        11.01        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-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 
       17.85        17.13        12.49        15.58         7.53        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        11.38        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-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       26.47       119.93       117.07        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       13.25         0.53        35.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       23.51        65.85        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       35.93        36.72        36.00        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
       18.18        10.98        19.33         9.93        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       12.00        42.77        32.98         8.42         9.70        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-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        15.39        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-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
        7.07        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        36.95        17.03        35.01         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         0.99        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-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         0.49         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         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        30.05        12.95        13.05        10.06       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-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        20.91        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-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         8.45        37.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39        32.19         0.66         0.69         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`18Q LOSS WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       46.65        42.90        33.53        22.06        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 
        1.02        13.02         1.02         8.05         0.00        29.00 
TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
        0.99        21.01        17.95        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       54.02         0.92        47.05        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-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        32.05        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       26.01        24.00         2.01        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       38.07         1.02        35.01        35.01        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-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.72        10.88         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
        0.20        21.44        17.82        19.33        50.37        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         0.33         0.10        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        70.16        15.62        51.32        21.14         2.93 
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 
       16.01        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 
       12.99        14.04        12.95        13.05        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 
       43.27        15.12         4.80        16.14        12.39        10.13 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         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 
       13.64         6.18        35.87        33.67        19.43       107.67 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 
       74.56        67.30        53.62        51.75        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        52.80        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-3892 
        8.02         1.02        12.03        19.99         0.99        13.02 
TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       14.01        20.98        36.03        49.97        61.97         1.45 
TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
        1.81         5.29        32.61        19.96         8.61        17.46 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        9.96         0.53         1.12 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            140.38             135.65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            19.035             19.330 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.3)"
[1] "hr=" "1.1"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   264 137
  18Q LOSS WILD-TYPE 178  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    264  137
  18Q LOSS WILD-TYPE  178   25
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON               264                178
  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       104         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          13         16         58         42       52
  18Q LOSS WILD-TYPE        13          5         21         12        9
                    vv
clus                 STAGE IVA STAGE IVB
  18Q LOSS MUTATED          24         1
  18Q LOSS WILD-TYPE         3         1
D73V4, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  58                 46
  STAGE IA                  0                  1
  STAGE II                 20                 16
  STAGE IIA               104                 67
  STAGE IIB                 4                  6
  STAGE IIC                 3                  0
  STAGE III                13                 13
  STAGE IIIA               16                  5
  STAGE IIIB               58                 21
  STAGE IIIC               42                 12
  STAGE IV                 52                  9
  STAGE IVA                24                  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
  18Q LOSS MUTATED    11  66 282  44
  18Q LOSS WILD-TYPE   9  41 131  22
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               11                  9
  T2               66                 41
  T3              282                131
  T4               44                 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
  18Q LOSS MUTATED   201 112  88
  18Q LOSS WILD-TYPE 141  37  26
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              201                141
  N1              112                 37
  N2               88                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   285  75
  18Q LOSS WILD-TYPE 163  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    285   75
  18Q LOSS WILD-TYPE  163   11
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              285                163
  1               75                 11
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   185 219
  18Q LOSS WILD-TYPE 101 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    185  219
  18Q LOSS WILD-TYPE  101  103
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              185                101
  MALE                219                103
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                    248                            15
  18Q LOSS WILD-TYPE                  133                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                     126                             10
  18Q LOSS WILD-TYPE                    20                              3
D73V9, multiclass
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        248                133
  COLON MUCINOUS ADENOCARCINOMA                15                 45
  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"
D73V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     8 396
  18Q LOSS WILD-TYPE   1 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8  396
  18Q LOSS WILD-TYPE    1  203
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 8                  1
  YES              396                203
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   289   3  30  14
  18Q LOSS WILD-TYPE 150   2   6  15
D73V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              289                150
  R1                3                  2
  R2               30                  6
  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
  18Q LOSS MUTATED                                  1     6
  18Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          40   199
  18Q LOSS WILD-TYPE                        20    93
D73V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      40                 20
  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"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    41  17
  19P LOSS WILD-TYPE 427  98
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                58                525 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                 98 
$`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-AY-6196 TCGA-AZ-4616 
       26.01        39.98        41.00         0.20         0.20         5.13 
TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6675 TCGA-D5-5537 
       65.00         3.29       102.44        49.08        13.05        45.40 
TCGA-D5-6533 TCGA-D5-6537 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6808 TCGA-G4-6295 
        1.32         4.80        44.32         6.12        33.67         8.35 
TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 
       36.00        10.98        30.28        24.13        14.50        15.95 
TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6155 
       17.03         9.07        64.01         4.73        12.99        13.97 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6885 
       24.13        51.48         0.49        16.34        11.51        13.64 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       11.97        31.30        28.57        18.28 

$`19P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-3810 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-A6-6650 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-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        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-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-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        20.98        19.99        13.94 
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-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-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         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-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        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-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        15.02        15.02 
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-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         4.21        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-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 
       15.75        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        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        62.79        61.41        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         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        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        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       11.51        20.19        20.42        17.75        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        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-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
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-A50V 
       91.79        46.75        47.15        52.80        18.18        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        13.05        12.00 
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         9.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        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-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-3593 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-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        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-3882 
       29.98         1.02        32.98         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-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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95        36.03         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         0.49 
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         6.05         6.97         9.37        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
        7.17        10.98        11.01        15.02        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24       129.27        32.61 
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-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.31        16.41         8.61        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       17.46         8.45         9.96        37.51         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         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.2                0.0 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            102.44             140.38 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            17.655             19.070 
[1] "0.2 - 102.4 (17.7)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.6"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    40  22
  19P LOSS WILD-TYPE 402 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     40   22
  19P LOSS WILD-TYPE  402  140
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON                40                402
  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       161         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           4          2          6          9       10
  19P LOSS WILD-TYPE        22         19         73         45       51
                    vv
clus                 STAGE IVA STAGE IVB
  19P LOSS MUTATED           7         1
  19P LOSS WILD-TYPE        20         1
D74V4, 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                161
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 4                 22
  STAGE IIIA                2                 19
  STAGE IIIB                6                 73
  STAGE IIIC                9                 45
  STAGE IV                 10                 51
  STAGE IVA                 7                 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
  19P LOSS MUTATED     1   9  45   8
  19P LOSS WILD-TYPE  19  98 368  58
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 19
  T2                9                 98
  T3               45                368
  T4                8                 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
  19P LOSS MUTATED    23  16  24
  19P LOSS WILD-TYPE 319 133  90
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               23                319
  N1               16                133
  N2               24                 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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    38  17
  19P LOSS WILD-TYPE 410  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     38   17
  19P LOSS WILD-TYPE  410   69
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               38                410
  1               17                 69
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    30  33
  19P LOSS WILD-TYPE 256 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     30   33
  19P LOSS WILD-TYPE  256  289
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               30                256
  MALE                 33                289
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                     32                             7
  19P LOSS WILD-TYPE                  349                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                      21                              0
  19P LOSS WILD-TYPE                   125                             13
D74V9, multiclass
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         32                349
  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"
D74V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  61
  19P LOSS WILD-TYPE   7 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   61
  19P LOSS WILD-TYPE    7  538
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                  7
  YES               61                538
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    41   0   6   3
  19P LOSS WILD-TYPE 398   5  30  26
D74V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               41                398
  R1                0                  5
  R2                6                 30
  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"
D74V12, 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                        55   262
D74V13, 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                 55
  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"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    38  13
  19Q LOSS WILD-TYPE 430 102
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                51                532 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                102 
$`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       102.44        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-3608 TCGA-AG-4001 TCGA-AG-A011 TCGA-AG-A01Y TCGA-CI-6624 TCGA-DC-4745 
       15.95        36.03        37.02        64.01         4.73        10.98 
TCGA-DC-5869 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 
       12.99        24.13         0.49        16.34        11.51        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       31.30        28.57        18.28 

$`19Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-3810 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-A6-6142 
       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-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        20.98        19.99        13.94        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-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00         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-3869 
       32.05         0.99        31.07        31.07        53.00        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-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-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        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-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        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-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 
        4.21        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-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        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 
       83.80        22.36        62.79        61.41        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-6715 
        1.94         2.24         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-4950 
        0.26         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
       35.87        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        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-G4-6315 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.72        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-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        13.05        12.00        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         9.70        70.03 
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        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        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         0.49         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-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37        13.97        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        51.48        32.61 
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-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.31        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       13.64        17.46         8.45         9.96        37.51         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 
        0.46        55.76        47.08        26.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            102.44             140.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            21.990             19.055 
[1] "0.5 - 102.4 (22.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.4"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    35  19
  19Q LOSS WILD-TYPE 407 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     35   19
  19Q LOSS WILD-TYPE  407  143
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON                35                407
  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       159         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           4          1          5          8        7
  19Q LOSS WILD-TYPE        22         20         74         46       54
                    vv
clus                 STAGE IVA STAGE IVB
  19Q LOSS MUTATED           5         1
  19Q LOSS WILD-TYPE        22         1
D75V4, 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                159
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 4                 22
  STAGE IIIA                1                 20
  STAGE IIIB                5                 74
  STAGE IIIC                8                 46
  STAGE IV                  7                 54
  STAGE IVA                 5                 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
  19Q LOSS MUTATED     1   7  41   6
  19Q LOSS WILD-TYPE  19 100 372  60
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 19
  T2                7                100
  T3               41                372
  T4                6                 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
  19Q LOSS MUTATED    24  10  21
  19Q LOSS WILD-TYPE 318 139  93
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               24                318
  N1               10                139
  N2               21                 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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    37  12
  19Q LOSS WILD-TYPE 411  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     37   12
  19Q LOSS WILD-TYPE  411   74
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               37                411
  1               12                 74
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29  26
  19Q LOSS WILD-TYPE 257 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   26
  19Q LOSS WILD-TYPE  257  296
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               29                257
  MALE                 26                296
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                     28                             6
  19Q LOSS WILD-TYPE                  353                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                      18                              0
  19Q LOSS WILD-TYPE                   128                             13
D75V9, multiclass
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         28                353
  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"
D75V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  53
  19Q LOSS WILD-TYPE   7 546
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   53
  19Q LOSS WILD-TYPE    7  546
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 2                  7
  YES               53                546
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    39   0   4   3
  19Q LOSS WILD-TYPE 400   5  32  26
D75V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               39                400
  R1                0                  5
  R2                4                 32
  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
  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                        56   268
D75V13, 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                 56
  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"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    53  11
  20P LOSS WILD-TYPE 415 104
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                64                519 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                104 
$`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 
       75.25        11.74        21.99         2.01        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        13.51        11.51        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        13.05        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 
        0.99        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        10.06        57.24        16.41 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       31.30        28.57         0.46        26.43 

$`20P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         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-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-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-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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        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-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-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-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-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-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        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-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       35.01         1.02        33.04        35.01        26.01        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-6901 
        4.21        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-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        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 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        19.59        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         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-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-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        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.24        33.67        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
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-A5IV 
       46.75        47.15        52.80        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30         9.70        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        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        16.83        15.39        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       65.98        12.00         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        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         1.02        32.98         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-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 
       23.01        37.02        15.95        36.03         9.07        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97        61.97        41.00        38.04         0.49 
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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE 
       12.95        13.05         5.29       126.44        41.36       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-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-F5-6810 
       17.46        11.97         8.45         9.96        37.51         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 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.46               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             92.75             140.38 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            24.015             18.840 
[1] "0.5 - 92.8 (24.0)"  "0.0 - 140.4 (18.8)"
[1] "hr=" "1.2"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    42  24
  20P LOSS WILD-TYPE 400 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     42   24
  20P LOSS WILD-TYPE  400  138
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON                42                400
  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       153        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          2         13          6        6
  20P LOSS WILD-TYPE        23         19         66         48       55
                    vv
clus                 STAGE IVA STAGE IVB
  20P LOSS MUTATED           3         0
  20P LOSS WILD-TYPE        24         2
D76V4, 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                153
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                2                 19
  STAGE IIIB               13                 66
  STAGE IIIC                6                 48
  STAGE IV                  6                 55
  STAGE IVA                 3                 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
  20P LOSS MUTATED     1  10  48   8
  20P LOSS WILD-TYPE  19  97 365  58
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                 19
  T2               10                 97
  T3               48                365
  T4                8                 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
  20P LOSS MUTATED    35  21  11
  20P LOSS WILD-TYPE 307 128 103
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               35                307
  N1               21                128
  N2               11                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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    50   8
  20P LOSS WILD-TYPE 398  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     50    8
  20P LOSS WILD-TYPE  398   78
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               50                398
  1                8                 78
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    33  34
  20P LOSS WILD-TYPE 253 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     33   34
  20P LOSS WILD-TYPE  253  288
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               33                253
  MALE                 34                288
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                     38                             4
  20P LOSS WILD-TYPE                  343                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                      21                              3
  20P LOSS WILD-TYPE                   125                             10
D76V9, multiclass
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         38                343
  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"
D76V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  67
  20P LOSS WILD-TYPE   9 532
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   67
  20P LOSS WILD-TYPE    9  532
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  9
  YES               67                532
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    51   1   5   2
  20P LOSS WILD-TYPE 388   4  31  27
D76V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               51                388
  R1                1                  4
  R2                5                 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"
D76V12, 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                        53   263
D76V13, 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                 53
  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"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 464 113
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                577 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                113 
$`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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        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-A6-4107 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-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-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-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-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-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-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-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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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         4.21        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-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        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        75.25        50.37 
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        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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 
        1.94         2.24         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         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        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 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
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-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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        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        35.41        19.43       107.67        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        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        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        47.15        52.80 
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-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       31.30         9.70        30.28        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        12.72        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-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        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-3882 
       29.98         1.02        32.98         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-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         0.99        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         0.49         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         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
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-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-F5-6571 
       17.46        11.97         8.45         9.96        37.51        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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.75             140.38 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.16              19.07 
[1] "2.0 - 92.8 (16.2)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.4"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 436 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  436  162
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON                 6                436
  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       168        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         21         78         53       61
                    vv
clus                 STAGE IVA STAGE IVB
  20Q LOSS MUTATED           0         0
  20Q LOSS WILD-TYPE        27         2
D77V4, 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                168
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                0                 21
  STAGE IIIB                1                 78
  STAGE IIIC                1                 53
  STAGE IV                  0                 61
  STAGE IVA                 0                 27
  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  20 107 407  66
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                 20
  T2                0                107
  T3                6                407
  T4                0                 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
  20Q LOSS MUTATED     3   1   2
  20Q LOSS WILD-TYPE 339 148 112
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                3                339
  N1                1                148
  N2                2                112
[1] 3 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
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 442  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  442   86
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                442
  1                0                 86
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   3
  20Q LOSS WILD-TYPE 283 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    3
  20Q LOSS WILD-TYPE  283  319
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                283
  MALE                  3                319
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                      5                             1
  20Q LOSS WILD-TYPE                  376                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                       0                              0
  20Q LOSS WILD-TYPE                   146                             13
D77V9, multiclass
                                clus
vv                               20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          5                376
  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"
D77V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   6
  20Q LOSS WILD-TYPE   9 593
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    6
  20Q LOSS WILD-TYPE    9  593
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                  9
  YES                6                593
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   0   0   0
  20Q LOSS WILD-TYPE 434   5  36  29
D77V11, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                434
  R1                0                  5
  R2                0                 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"
D77V12, 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                        58   290
D77V13, 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                 58
  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"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   143  35
  21Q LOSS WILD-TYPE 325  80
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               178                405 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                 80 
$`21Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5665 
       43.76        43.76        37.05        14.53        30.44        22.06 
TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       29.16        20.61        21.76        24.39        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84         9.63         5.03         6.97        38.99         9.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3560 TCGA-AA-3660 
       19.07        34.03        26.01        14.01        19.99        78.08 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 
       37.05        19.00        36.00        10.06        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 
       14.93        10.06         0.99        17.03        24.03        18.05 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 
       24.00        20.98         2.01        21.99         7.96        13.94 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D 
       38.04        27.02        42.02        21.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6890 
       32.02        31.00        51.98        39.98        41.00         0.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 
       22.42         0.20        16.44        14.50        16.31         0.20 
TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       17.85         5.13        65.00        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 
        3.19         2.24         2.14         3.29         0.26        49.08 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       21.99        20.02         8.02        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 
       22.98        16.01         5.03        15.02        14.04        29.03 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 
       15.02        11.08        11.01        45.40        17.75         1.32 
TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A 
       13.41        49.91       140.38         7.50       131.51        26.47 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
        8.61        13.38        35.87         1.55        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6314 TCGA-G4-6315 
       33.67         0.53        35.41         8.35        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA 
       36.00        26.43        91.79        46.75        18.18         9.93 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 
       13.05        42.77        24.13        39.48        17.23        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       15.39        20.02        10.39        86.63        11.84        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 
        7.07        36.03        24.00        46.03        34.03        12.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 
        6.05        19.99        29.98        19.99        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N 
       48.03        19.99        36.03        17.03        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       70.03        64.01        10.98        38.96        61.97        41.00 
TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6158 
        0.69         4.73        13.97        10.98        13.97        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       13.05        10.06       126.44        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       32.61        20.55        20.91        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       16.41        11.97         8.45        31.30         0.39         0.66 
TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.53         0.76        18.28        26.43 

$`21Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       16.57        37.25        37.02        34.65        36.53        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-A6-5666 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-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.18        24.16        24.69        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-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
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-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
        0.00        29.00        29.00        12.99         0.99        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-3662 TCGA-AA-3663 
       20.98        13.94        19.99        61.02         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-3696 TCGA-AA-3697 
       47.01        15.02        11.01         5.98         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-3845 TCGA-AA-3846 
        1.02        17.98        15.95        36.95         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       12.99        33.01        26.01        24.00         2.01        34.03 
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-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98        15.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37         4.21        56.55         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.46         0.92        27.09         0.95        15.75 
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        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       11.74         1.94         3.06         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        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         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5349 
       23.05        37.02        25.02        26.04        29.06        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         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-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       92.75        13.32        12.59        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        81.37       119.93        35.97 
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        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 
       13.45         6.18        16.31        13.25        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21        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        51.75        45.11        39.42 
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        47.15 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       52.80        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.00        29.46        32.98         8.42        31.30         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       30.28        70.03        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 
       37.74        10.39        16.83        65.98        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
        8.02        20.05         1.02         2.01        50.04         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       14.01        32.02        28.04        14.04         1.02         0.99 
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         0.49         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         6.05         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        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC 
       15.02        36.00        30.05        12.95         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        37.51        28.57        32.19         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.2                0.0 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            140.38             139.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             19.53              19.07 
[1] "0.2 - 140.4 (19.5)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1"  
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   122  67
  21Q LOSS WILD-TYPE 320  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    122   67
  21Q LOSS WILD-TYPE  320   95
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON               122                320
  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        50         1         1
  21Q LOSS WILD-TYPE      77        1       25       121         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           7          9         27         22       24
  21Q LOSS WILD-TYPE        19         12         52         32       37
                    vv
clus                 STAGE IVA STAGE IVB
  21Q LOSS MUTATED           7         0
  21Q LOSS WILD-TYPE        20         2
D78V4, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  27                 77
  STAGE IA                  0                  1
  STAGE II                 11                 25
  STAGE IIA                50                121
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 7                 19
  STAGE IIIA                9                 12
  STAGE IIIB               27                 52
  STAGE IIIC               22                 32
  STAGE IV                 24                 37
  STAGE IVA                 7                 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
  21Q LOSS MUTATED     6  34 132  18
  21Q LOSS WILD-TYPE  14  73 281  48
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                6                 14
  T2               34                 73
  T3              132                281
  T4               18                 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
  21Q LOSS MUTATED    92  51  47
  21Q LOSS WILD-TYPE 250  98  67
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               92                250
  N1               51                 98
  N2               47                 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"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   137  28
  21Q LOSS WILD-TYPE 311  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    137   28
  21Q LOSS WILD-TYPE  311   58
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              137                311
  1               28                 58
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    92  98
  21Q LOSS WILD-TYPE 194 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     92   98
  21Q LOSS WILD-TYPE  194  224
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               92                194
  MALE                 98                224
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                    114                             8
  21Q LOSS WILD-TYPE                  267                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                      62                              3
  21Q LOSS WILD-TYPE                    84                             10
D78V9, multiclass
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        114                267
  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"
D78V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 186
  21Q LOSS WILD-TYPE   5 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  186
  21Q LOSS WILD-TYPE    5  413
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  5
  YES              186                413
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   137   1  12   6
  21Q LOSS WILD-TYPE 302   4  24  23
D78V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              137                302
  R1                1                  4
  R2               12                 24
  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"
D78V12, 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                          15    95
  21Q LOSS WILD-TYPE                        45   197
D78V13, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      15                 45
  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"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   144  43
  22Q LOSS WILD-TYPE 324  72
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               187                396 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                43                 72 
$`22Q LOSS MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
        4.80        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-A6-5657 
       13.94        16.57        34.65        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 
       30.44        29.19        23.61        22.52        20.61        21.76 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 
       23.87        61.84        56.25         9.63         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        9.07        24.03        37.05        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 
       33.99        21.01        13.02        19.99        13.94         6.05 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 
        2.01        50.04        37.05        85.05        10.06        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03        10.06        33.07        32.05 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       12.99         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       26.01         7.96        13.94        34.03        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       17.03        14.99        15.02        33.04        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       39.98        41.00        40.96         5.79        22.42         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4323 
       16.44        14.50        16.31        15.75        17.85         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.65         5.13        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6748 
        1.94         3.06         0.26         1.35        49.08         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       25.02         8.02        29.06        30.08         5.03        15.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       15.02        11.08        11.01        45.40        13.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
        1.32        43.27        15.12        17.85        12.49         7.53 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       13.41        11.38        12.59       140.38       131.51         6.12 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 
       26.47        13.38         1.55        16.24        13.25         8.35 
TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       82.39        45.11        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YW 
       18.18        10.98        19.33         9.93        42.77        29.46 
TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
        9.70        13.55        14.50        15.39        10.39        65.98 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3728 
       12.00        32.02         7.07        20.05        34.03        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 
        1.02        19.99         1.02         1.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       14.04        25.97        12.00        10.98         1.94        38.96 
TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 
        0.49         0.72        10.19         6.05         4.73        13.97 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       10.98        12.99        13.97        10.98        30.05        13.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 
       10.06        41.36        51.48         2.40        20.55        17.69 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 
       16.41        28.57         0.39         0.66         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`22Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       24.33        37.05        37.25        37.02        32.45        32.91 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        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-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-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
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-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       29.00         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       23.01        20.98        19.99        61.02        78.08         6.97 
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-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-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        14.93         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 
       36.03         0.99        31.07        53.00        29.98        31.00 
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-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       16.08        34.06        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       38.04         4.01         0.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01         1.02        35.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        22.03        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         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72        27.42        10.88         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95         0.20        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        75.25        50.37        58.39        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        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         2.24         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         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
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        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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        11.51        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        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         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        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.45         6.18        35.87        16.31        29.59        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        35.41        19.43       107.67        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 
       51.75        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        47.15        52.80        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        13.05        12.00        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        30.28        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        19.10        12.72        37.74        10.39        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 
       20.02        86.63        11.84        36.03         8.02        36.03 
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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 
        0.99        32.98         0.99         0.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       13.02        35.01        14.01        48.03        32.02        28.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        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-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        70.03        64.01        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         1.45         0.69        26.43         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         9.37        78.12         7.17        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        36.00        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24       129.27        24.13        32.61         0.49 
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-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-F5-6811 
       11.97         8.45         9.96        37.51        31.30        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.46        55.76        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.2                0.0 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.38             139.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            17.030             19.975 
[1] "0.2 - 140.4 (17.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.5"
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   142  55
  22Q LOSS WILD-TYPE 300 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    142   55
  22Q LOSS WILD-TYPE  300  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON               142                300
  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        46         1         1
  22Q LOSS WILD-TYPE      80        1       27       125         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           9         11         29         22       30
  22Q LOSS WILD-TYPE        17         10         50         32       31
                    vv
clus                 STAGE IVA STAGE IVB
  22Q LOSS MUTATED          11         0
  22Q LOSS WILD-TYPE        16         2
D79V4, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  24                 80
  STAGE IA                  0                  1
  STAGE II                  9                 27
  STAGE IIA                46                125
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 9                 17
  STAGE IIIA               11                 10
  STAGE IIIB               29                 50
  STAGE IIIC               22                 32
  STAGE IV                 30                 31
  STAGE IVA                11                 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
  22Q LOSS MUTATED     4  31 137  27
  22Q LOSS WILD-TYPE  16  76 276  39
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                 16
  T2               31                 76
  T3              137                276
  T4               27                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  22Q LOSS MUTATED    85  67  46
  22Q LOSS WILD-TYPE 257  82  68
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               85                257
  N1               67                 82
  N2               46                 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
  22Q LOSS MUTATED   133  40
  22Q LOSS WILD-TYPE 315  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    133   40
  22Q LOSS WILD-TYPE  315   46
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              133                315
  1               40                 46
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    92 107
  22Q LOSS WILD-TYPE 194 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     92  107
  22Q LOSS WILD-TYPE  194  215
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               92                194
  MALE                107                215
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                    132                            10
  22Q LOSS WILD-TYPE                  249                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                      51                              4
  22Q LOSS WILD-TYPE                    95                              9
D79V9, multiclass
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        132                249
  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"
D79V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 195
  22Q LOSS WILD-TYPE   5 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  195
  22Q LOSS WILD-TYPE    5  404
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 4                  5
  YES              195                404
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   135   2  15  11
  22Q LOSS WILD-TYPE 304   3  21  18
D79V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              135                304
  R1                2                  3
  R2               15                 21
  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"
D79V12, 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                          22    91
  22Q LOSS WILD-TYPE                        38   201
D79V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      22                 38
  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"

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    60  22
  XP LOSS WILD-TYPE 408  93
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               82               501 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               22                93 
$`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        13.38        33.67         8.35        65.85        36.72 
TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-WS-AB45 
       26.04        10.98         9.93        15.65        12.00        70.03 
TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3593 
       19.10        11.84        12.00        32.02        24.00        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01Y 
        2.01         6.05        32.98        13.94        23.01        64.01 
TCGA-AG-A02X TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 
       41.00         0.49        10.19        13.97        30.05         5.29 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-7002 TCGA-F5-6571 
       57.24       129.27        11.97        31.30 

$`XP LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        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-A5ZU TCGA-AA-3488 
       19.66        20.28        16.24        24.92         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-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-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        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-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-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-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-3966 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-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        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02H 
       26.01        37.02        39.06        51.98         2.96         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         4.21        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-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        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 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10        29.56         5.23         1.94         2.24 
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         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       14.99        12.99        13.02        14.04        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 
       13.51        11.51        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         7.53        12.39        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        35.41        19.43       107.67 
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-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        12.79        13.05        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30         9.70        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        12.72        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-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       65.98        36.03         8.02         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02        46.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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 
        0.99        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         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       12.00        15.02        36.00        10.98        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       10.06       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        37.51        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         0.46        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            139.17 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           22.485            19.040 
[1] "0.2 - 140.4 (22.5)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.2"
D80V2, continuous
D80V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    62  26
  XP LOSS WILD-TYPE 380 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     62   26
  XP LOSS WILD-TYPE  380  136
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON               62               380
  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        24         0         0
  XP LOSS WILD-TYPE      92        1       31       147        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         20         68         43       47
                   vv
clus                STAGE IVA STAGE IVB
  XP LOSS MUTATED           3         1
  XP LOSS WILD-TYPE        24         1
D80V4, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 12                92
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               24               147
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                5                21
  STAGE IIIA               1                20
  STAGE IIIB              11                68
  STAGE IIIC              11                43
  STAGE IV                14                47
  STAGE IVA                3                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
  XP LOSS MUTATED     1  12  65  11
  XP LOSS WILD-TYPE  19  95 348  55
D80V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                19
  T2              12                95
  T3              65               348
  T4              11                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
  XP LOSS MUTATED    42  21  26
  XP LOSS WILD-TYPE 300 128  88
D80V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              42               300
  N1              21               128
  N2              26                88
[1] 3 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
  XP LOSS MUTATED    61  19
  XP LOSS WILD-TYPE 387  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     61   19
  XP LOSS WILD-TYPE  387   67
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              61               387
  1              19                67
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    39  50
  XP LOSS WILD-TYPE 247 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   50
  XP LOSS WILD-TYPE  247  272
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              39               247
  MALE                50               272
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP LOSS MUTATED                     56                             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
D80V9, multiclass
                                clus
vv                               XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        56               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"
D80V10, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     1  88
  XP LOSS WILD-TYPE   8 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   88
  XP LOSS WILD-TYPE    8  511
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                1                 8
  YES              88               511
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    62   0   6   4
  XP LOSS WILD-TYPE 377   5  30  25
D80V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              62               377
  R1               0                 5
  R2               6                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"
D80V12, 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                          11    36
  XP LOSS WILD-TYPE                        49   256
D80V13, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     11                49
  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"

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    55  17
  XQ LOSS WILD-TYPE 413  98
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               72               511 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17                98 
$`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        15.75        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         2.01        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        36.72        26.04        10.98         9.93 
TCGA-NH-A8F8 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 
       12.00        19.10        11.84        12.00        32.02        24.00 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01N 
        2.01         6.05        32.98        13.94        23.01        31.00 
TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 
       64.01        41.00         0.49        10.19        13.97        30.05 
TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6571 
        5.29        57.24       129.27        32.61        11.97        31.30 

$`XQ LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        44.91        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-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        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-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-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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        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-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-3680 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        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-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-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-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       27.02        19.07        27.02        13.94        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        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        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        75.25        50.37        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        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01        29.56         5.23         1.94         2.24         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       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        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        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 
       13.51        11.51        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         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       92.75        13.32        12.59         7.50        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-F4-6459 
       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 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.00        26.43        22.09 
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        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       52.80        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 
       13.05        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        9.70        30.28        70.03        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        12.72        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-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       36.03         8.02         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        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 
        0.99        20.98         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 
       36.03         9.07         1.02        12.00        70.03        10.98 
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-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 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        10.98        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        24.13        51.48         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-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
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         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.2               0.0 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           140.38            139.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            22.50             19.04 
[1] "0.2 - 140.4 (22.5)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.2"
D81V2, continuous
D81V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    50  26
  XQ LOSS WILD-TYPE 392 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     50   26
  XQ LOSS WILD-TYPE  392  136
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON               50               392
  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        20         0         0
  XQ LOSS WILD-TYPE      93        1       31       151        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         19         71         44       46
                   vv
clus                STAGE IVA STAGE IVB
  XQ LOSS MUTATED           3         0
  XQ LOSS WILD-TYPE        24         2
D81V4, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               20               151
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               2                19
  STAGE IIIB               8                71
  STAGE IIIC              10                44
  STAGE IV                15                46
  STAGE IVA                3                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
  XQ LOSS MUTATED     1  13  53  10
  XQ LOSS WILD-TYPE  19  94 360  56
D81V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                19
  T2              13                94
  T3              53               360
  T4              10                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
  XQ LOSS MUTATED    37  19  21
  XQ LOSS WILD-TYPE 305 130  93
D81V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              37               305
  N1              19               130
  N2              21                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"
D81V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    51  19
  XQ LOSS WILD-TYPE 397  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     51   19
  XQ LOSS WILD-TYPE  397   67
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              51               397
  1              19                67
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    35  42
  XQ LOSS WILD-TYPE 251 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     35   42
  XQ LOSS WILD-TYPE  251  280
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              35               251
  MALE                42               280
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                     44                             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
D81V9, multiclass
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        44               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"
D81V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  76
  XQ LOSS WILD-TYPE   8 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   76
  XQ LOSS WILD-TYPE    8  523
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 8
  YES              76               523
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    50   0   7   4
  XQ LOSS WILD-TYPE 389   5  29  25
D81V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              50               389
  R1               0                 5
  R2               7                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"
D81V12, 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                           9    31
  XQ LOSS WILD-TYPE                        51   261
D81V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      9                51
  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"
