[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/11541489/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/11549101/transformed.cor.cli.txt"

nPatients in clinical file=620, in cluster file=615, common to both=604
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 604
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               555 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               555 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               488 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               488 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              119               485 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              119               485 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              117               487 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              117               487 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               532 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               532 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               97               507 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               97               507 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               584 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               584 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               583 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               583 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               501 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               501 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               65               539 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               65               539 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              122               482 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              122               482 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              109               495 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              109               495 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              345               259 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              345               259 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              309               295 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              309               295 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              167               437 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              167               437 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              310               294 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              310               294 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              120               484 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              120               484 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               503 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              101               503 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                46                558 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                46                558 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                578 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                578 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                83                521 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                83                521 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                75                529 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                75                529 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                477 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               127                477 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                493 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               111                493 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               362                242 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               362                242 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                42                562 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                42                562 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                589 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                589 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               145                459 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               145                459 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               143                461 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               143                461 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                568 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                568 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               110                494 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               110                494 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                571 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                571 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                20                584 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                20                584 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               102                502 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               102                502 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               111                493 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               111                493 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               347                257 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               347                257 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               455                149 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               455                149 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                572 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                572 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                581 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                581 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              104               500 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              104               500 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              134               470 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              134               470 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               77               527 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               77               527 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               587 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               587 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               590 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               590 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               537 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               537 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               561 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               561 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              188               416 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              188               416 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              182               422 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              182               422 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               82               522 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               82               522 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              116               488 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              116               488 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               559 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               559 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               536 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               536 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               600 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               600 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              213               391 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              213               391 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               569 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               569 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74               530 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74               530 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               74               530 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               74               530 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                504 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               100                504 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               109                495 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               109                495 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                530 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                530 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                513 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                513 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                534 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                70                534 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                69                535 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                69                535 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                584 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                584 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               201                403 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               201                403 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               222                382 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               222                382 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                564 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                564 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                562 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                562 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               334                270 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               334                270 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                511 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                511 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               372                232 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               372                232 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               401                203 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               401                203 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                541 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                63                541 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                549 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                549 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                65                539 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                65                539 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                598 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                598 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               190                414 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               190                414 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               196                408 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               196                408 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               527 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               527 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 604 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
         154          160         1126         1419         1331         1321 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
         711          541         1286         1366         1068         1387 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
          NA          472         1127         1133          488         1054 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
        1111           NA          987         1001          962          926 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
         888         1020          718          672          671          995 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         887          824          685          734          255          763 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
         766          735          627          662          751          742 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
         726          612          598          617           NA           NA 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
          NA         1595          293           NA           31           NA 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
          31         1127           31         1065         1765         1946 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
         212           31           NA         1186           31          276 
TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
         731           NA         1127         1096          245          580 
TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
          NA           NA          580         1035          882          882 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
         791          395           30          426         1034          639 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
          NA          730          546          911          700          638 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
         608          424          608         1856         2375          184 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
         212         1643           NA          426           28         1522 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 
        1431         1430          457           NA          182           NA 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 
        1127          578           NA           NA           NA           NA 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        2587          821           NA          579           30           30 
TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        1066           NA           NA          761           31          547 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
         485         1186         1124         1126          454           NA 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
         518           30           NA         1006           NA         1096 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
         975           30          945          945         1612          518 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 
         731           NA          912           NA          549          943 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
          NA          395          730         1004          791          730 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
          NA          638         1035           61          669          489 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        1551          397         1036          791          761          730 
TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
         822           NA          580           NA          822          424 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
        1157          578          913         1035          549          549 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
         518           NA          822         1278           30          518 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
         456          669         1064          457          457           30 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
         974          365          943          943           NA           31 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1065           31         1005         1065          791         1126 
TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
          NA           NA         1581           NA         1216           NA 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
          NA           28           NA         1247         1216           NA 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
        1246            2          650          128         1720           24 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
          22           48           31            3           23            6 
TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
          NA           13           14           28          441          824 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
          NA           NA          479            6          652          542 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
         158          168          209         2289         1532         1776 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
          NA           NA         1002           NA         2549           NA 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        1977           NA         1868           NA           NA           NA 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
          NA           NA           NA           NA           NA           NA 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
          68           93           65           99          100            2 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
           8           10            3           41          534         3116 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1227         2134          475         1466         1561          669 
TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
          NA           NA           NA           89           61         3780 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
         701          609         1126          244          792          244 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
         822          396          884          670          699          915 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
         487          457           NA          457          457          518 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
         457          365          427          883          488          669 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
         456          395          396          457          427          335 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
         394          397          337          337          335          306 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
         366          456          373          596          411          350 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
         614          621          540          555           40          241 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
         460          543          137          521          380          491 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
         474          229          377          308          378          435 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
         275          287          354          408           46          365 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
         346          312         3641          743         1162         3974 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
        2821         1518          405          383         4270          228 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        1348         4000         4126          236         4233          186 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
         427          805         2475         3648         1094         1849 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
        3561         2988         2895           NA          407           NA 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
         415          409           NA         1091           47          496 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
         900          494         1024           39           16         1077 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
         591         3275           NA          254         2506           NA 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        2268         1310         1882         1631         1359         1674 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
        1574         1372         1199         1093         1117         1095 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
         804          672          792          419         1089          796 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
        2792           NA         1434         1606          125           NA 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
         320           85          182          170           40          158 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
         167          821          526          202          449          921 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        2038          734          546          524         1309          412 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
         581          387         1148           NA          441          257 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
         468          609          316         2635         2007          360 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
          NA          365          974          244          215           31 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
          61           NA           31         1400           NA           NA 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 
        1035           NA         1522          366          184           NA 
TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
          NA           30          485          608           NA          608 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
          NA          243           30          912           31         1003 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
          30           30           NA          608           31           NA 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1124          518          396         1065          426           31 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1461           NA          974          608          853         1096 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 
         427           31          518           NA           NA           30 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
         638          424          183          790          700         1126 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
         485         1096          276           31          365          943 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        2130         1947          334           NA         1520           NA 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
          NA         1885         1247         1157           15           44 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
          21           22          140           55          310          184 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
         184           NA          212          285          144          425 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        1826          243          334          335          457          395 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
         365          425          457         1095          216          914 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
         394          397          306          161         3846         1258 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        1741         3932          734         1566          992           15 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
          73          625          607          636          517          556 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
         482          538          497          496          499          262 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         350          328          415          531          364          257 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
          NA         1141          952          452           12           31 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
          20           21           16           34           23           14 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=345,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
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:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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.
Variable 21:'BATCH.NUMBER':	nDistinctValues=32,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [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"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 604 columns, 1 survival variables, and 12 non-survival variables.
AGE, 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 
 20 105 412  65 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 105 412  65 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 105 412  65 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 105 412  65 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
341 148 112 
[1] "table(vv)"
vv
 N0  N1  N2 
341 148 112 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
341 148 112 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
341 148 112 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
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    34  13
  1P GAIN WILD-TYPE 432  96
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               47               528 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13                96 
$`1P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-6654 TCGA-AA-3552 
       37.02        44.91        45.60        15.52        23.87        13.02 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3973 TCGA-AA-A01D 
       54.02         2.01        15.02        19.00        13.05         0.99 
TCGA-AA-A02E TCGA-AD-6888 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 TCGA-AZ-4684 
        2.96         4.21         0.20         5.52        22.36        65.00 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
        3.06         0.26        48.20         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       14.99        15.12         7.53        10.13        12.43        14.30 
TCGA-DM-A0X9 TCGA-DM-A28M TCGA-NH-A50T TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2692 
      119.70        95.18         4.11        26.99        30.28        13.55 
TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-A026 TCGA-AG-A02G TCGA-DC-6156 
       14.50        32.02        46.03         1.94        38.96        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-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       17.79        42.28        35.11        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        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-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
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-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-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        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-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         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        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-5256 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         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-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        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-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        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         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         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         1.28         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 
       43.07        61.87        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-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80        10.98        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
        5.98         5.59         1.32         5.19         5.49        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        67.00        24.13        17.95        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         8.45 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-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-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-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         4.60 
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        60.03         7.99        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         7.10 
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-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 
       11.51        13.64        17.46        11.97        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         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 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           119.70            140.38 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            14.99             18.05 
[1] "0.2 - 119.7 (15.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.6"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    35  12
  1P GAIN WILD-TYPE 403 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     35   12
  1P GAIN WILD-TYPE  403  150
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON               35               403
  RECTUM              12               150
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P GAIN MUTATED         6        0        2        12         1         0
  1P GAIN WILD-TYPE      96        1       34       159         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          3          4          7        7
  1P GAIN WILD-TYPE        25         18         74         46       54
                   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                  6                96
  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                74
  STAGE IIIC               7                46
  STAGE IV                 7                54
  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  98 380  57
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               2                18
  T2               7                98
  T3              32               380
  T4               8                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
  1P GAIN MUTATED    23  12  13
  1P GAIN WILD-TYPE 318 136  99
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              23               318
  N1              12               136
  N2              13                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  1P GAIN MUTATED    29   9   2   0   7
  1P GAIN WILD-TYPE 417  65   8   2  56
D1V7, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               29               417
  M1                9                65
  M1A               2                 8
  M1B               0                 2
  MX                7                56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    20  29
  1P GAIN WILD-TYPE 263 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20   29
  1P GAIN WILD-TYPE  263  292
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              20               263
  MALE                29               292
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                     33                             2
  1P GAIN WILD-TYPE                  345                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                       9                              3
  1P GAIN WILD-TYPE                   137                             10
D1V9, multiclass
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        33               345
  COLON MUCINOUS ADENOCARCINOMA                2                57
  RECTAL ADENOCARCINOMA                        9               137
  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   8 547
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   48
  1P GAIN WILD-TYPE    8  547
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1                 8
  YES              48               547
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    34   1   5   4
  1P GAIN WILD-TYPE 402   4  31  25
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              34               402
  R1               1                 4
  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"
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                        51   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                51
  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 381  83
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              111               464 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               26                83 
$`1Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       37.02        43.76        44.91        35.11        45.60        15.52 
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-3858 TCGA-AA-3866 
       15.02        19.00         5.03         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A01D 
       27.02        12.99        33.01        13.05        27.02         0.99 
TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y TCGA-AD-6888 TCGA-AU-3779 
       35.01        26.01         2.96        39.98         4.21        14.50 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 
        0.20         5.52        22.36        65.00        12.10        11.74 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 
        3.06         0.26        48.20        37.02         8.02        22.98 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-6533 
       15.02         5.03        15.02        14.04        14.99         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.12        17.85         7.53        10.13        12.43        14.30 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6459 
      119.70        92.75        81.37        35.97        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 
       13.38        11.11        35.41        82.39        74.56        61.87 
TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2692 
       39.42         4.11         5.98        26.99        30.28        13.55 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 
       14.50        15.39        10.39        32.02        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3999 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 
        6.05        28.04        36.03        31.00        70.03        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.96        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-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        13.94        37.05        37.25        16.04        34.65 
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-A6-6653 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-3489 TCGA-AA-3492 
       24.92        61.84        52.44         9.63         1.02         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-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-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        19.99        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
        6.97        14.01         0.92        50.04        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        37.05        36.00        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        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-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       17.03        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       25.02        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         6.87        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-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-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-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         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-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
        7.92         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-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-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6463 
       26.47       119.93        60.79       117.07        98.24        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-F4-6856 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       28.21         8.35        23.51        43.07        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        51.75        45.11        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-A50U TCGA-NH-A50V 
       91.79        46.75        47.15        52.80        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
        2.79         5.59         1.32         5.19         5.49        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        67.00        24.13        17.95        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         8.45 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
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-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-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 
       15.95         9.07         1.02        12.00        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97        41.00         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        10.98        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.20              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            140.38 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           15.390            17.965 
[1] "0.2 - 129.3 (15.4)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    79  35
  1Q GAIN WILD-TYPE 359 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     79   35
  1Q GAIN WILD-TYPE  359  127
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON               79               359
  RECTUM              35               127
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q GAIN MUTATED        13        0        7        26         2         0
  1Q GAIN WILD-TYPE      89        1       29       145         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           4          4         15         15       20
  1Q GAIN WILD-TYPE        22         17         63         38       41
                   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                 13                89
  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                63
  STAGE IIIC              15                38
  STAGE IV                20                41
  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  90 336  44
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               4                16
  T2              15                90
  T3              76               336
  T4              21                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    53  30  31
  1Q GAIN WILD-TYPE 288 118  81
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              53               288
  N1              30               118
  N2              31                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  1Q GAIN MUTATED    76  23   3   0  12
  1Q GAIN WILD-TYPE 370  51   7   2  51
D2V7, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               76               370
  M1               23                51
  M1A               3                 7
  M1B               0                 2
  MX               12                51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    50  66
  1Q GAIN WILD-TYPE 233 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     50   66
  1Q GAIN WILD-TYPE  233  255
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              50               233
  MALE                66               255
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                     73                             6
  1Q GAIN WILD-TYPE                  305                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                      30                              4
  1Q GAIN WILD-TYPE                   116                              9
D2V9, multiclass
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        73               305
  COLON MUCINOUS ADENOCARCINOMA                6                53
  RECTAL ADENOCARCINOMA                       30               116
  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   6 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  113
  1Q GAIN WILD-TYPE    6  482
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                3                 6
  YES             113               482
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    80   1  11   5
  1Q GAIN WILD-TYPE 356   4  25  24
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              80               356
  R1               1                 4
  R2              11                25
  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                        46   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                46
  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  23
  2P GAIN WILD-TYPE 376  86
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              113               462 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23                86 
$`2P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
        5.06        37.02        16.04        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         0.99        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        17.03        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         1.58         1.02         0.10         0.43 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 
       16.31         0.20         6.87         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 
       14.99        11.51         4.50        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         4.11         1.32         5.19 
TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 
       17.29        30.28        24.13        17.95        17.23         8.45 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 
       86.63        65.98        36.03        46.03        34.03        19.99 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N 
       19.99         1.02         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         4.60        10.19        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 
       10.98        12.99        12.00        15.02        36.00        13.05 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 
      129.27        51.48        20.55        16.31        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       37.51         0.46        18.28        55.76        47.08 

$`2P GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
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        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       37.05        37.25        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       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-A6-6653 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        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1.02        37.05        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
       36.03         8.05        19.07        19.07        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-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-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        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-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        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         0.76         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-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        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        48.20        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 
        8.02        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         7.92        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 
        1.28         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        43.07        61.87        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        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.59         5.49        26.99         6.64        14.76        67.00 
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-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 
       14.50        15.39        20.02        10.39        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         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-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-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-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        9.07         1.02        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-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-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 
        9.37         4.73        13.97        11.01        15.02        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        24.13        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6641 
        0.66         0.69         0.53         1.12         0.76        26.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            140.38 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           17.030            18.015 
[1] "0.1 - 129.3 (17.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    78  41
  2P GAIN WILD-TYPE 360 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     78   41
  2P GAIN WILD-TYPE  360  121
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON               78               360
  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      86        1       28       142        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          3         19         14       11
  2P GAIN WILD-TYPE        20         18         59         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                86
  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                59
  STAGE IIIC              14                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  87  10
  2P GAIN WILD-TYPE  18  86 325  55
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               2                18
  T2              19                86
  T3              87               325
  T4              10                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
  2P GAIN MUTATED    58  29  30
  2P GAIN WILD-TYPE 283 119  82
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              58               283
  N1              29               119
  N2              30                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  2P GAIN MUTATED    80  15   3   1  17
  2P GAIN WILD-TYPE 366  59   7   1  46
D3V7, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               80               366
  M1               15                59
  M1A               3                 7
  M1B               1                 1
  MX               17                46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    60  59
  2P GAIN WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     60   59
  2P GAIN WILD-TYPE  223  262
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              60               223
  MALE                59               262
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                     73                             5
  2P GAIN WILD-TYPE                  305                            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               305
  COLON MUCINOUS ADENOCARCINOMA                5                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     3 116
  2P GAIN WILD-TYPE   6 479
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3  116
  2P GAIN WILD-TYPE    6  479
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                3                 6
  YES             116               479
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    83   3   5  10
  2P GAIN WILD-TYPE 353   2  31  19
D3V11, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              83               353
  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                          15    67
  2P GAIN WILD-TYPE                        41   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                     15                41
  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  24
  2Q GAIN WILD-TYPE 379  85
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              111               464 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               24                85 
$`2Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 
        5.06        37.02        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         0.99        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         1.58         1.02         0.10         0.43        16.31 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
        6.87         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        14.99        11.51         4.50        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         4.11 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
        1.32         5.19        17.29        30.28        24.13        17.95 
TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       17.23        10.39         8.45        15.39        86.63        65.98 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 
       36.03        46.03        34.03        19.99        19.99         1.02 
TCGA-AG-3898 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       48.03         1.02         0.99        12.00        31.00        70.03 
TCGA-AG-A032 TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       38.04         4.60        10.19        60.03         7.99        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 
       12.00        15.02        36.00        13.05       129.27         2.40 
TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 
       20.55        16.31        13.64         9.96        37.51         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.46        18.28        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
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        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        16.04        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        52.44         9.63         5.03         1.02 
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-3530 TCGA-AA-3538 
       37.05        36.03         8.05        19.07        19.07        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        2.01        14.01         0.92        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        0.07        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.20        21.44        17.82         5.19         5.52        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        48.20        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         8.02        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         7.92        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         1.28 
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        43.07        61.87        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        10.52         2.79         5.98         5.59         5.49 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       26.99         6.64        14.76        67.00        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-6672 
       19.10        12.72        37.74        14.50        20.02        10.39 
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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        2.01        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 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-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       29.98         1.02        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
       36.95        17.03        13.02        35.01        14.01        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-4745 TCGA-DC-4749 
        6.97         9.37         4.73        13.97        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        13.97         7.10        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         0.49        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-F5-6571 TCGA-F5-6702 
       10.78        17.46        11.97         8.45        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.10              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            140.38 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           17.130            17.965 
[1] "0.1 - 129.3 (17.1)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    74  43
  2Q GAIN WILD-TYPE 364 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     74   43
  2Q GAIN WILD-TYPE  364  119
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON               74               364
  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      86        1       28       144        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           7          3         18         15       12
  2Q GAIN WILD-TYPE        19         18         60         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                86
  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                60
  STAGE IIIC              15                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  85  10
  2Q GAIN WILD-TYPE  18  86 327  55
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                18
  T2              19                86
  T3              85               327
  T4              10                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
  2Q GAIN MUTATED    56  28  31
  2Q GAIN WILD-TYPE 285 120  81
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              56               285
  N1              28               120
  N2              31                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  2Q GAIN MUTATED    79  15   2   1  18
  2Q GAIN WILD-TYPE 367  59   8   1  45
D4V7, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               79               367
  M1               15                59
  M1A               2                 8
  M1B               1                 1
  MX               18                45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    60  57
  2Q GAIN WILD-TYPE 223 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     60   57
  2Q GAIN WILD-TYPE  223  264
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              60               223
  MALE                57               264
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                     69                             5
  2Q GAIN WILD-TYPE                  309                            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               309
  COLON MUCINOUS ADENOCARCINOMA                5                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     4 113
  2Q GAIN WILD-TYPE   5 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4  113
  2Q GAIN WILD-TYPE    5  482
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                4                 5
  YES             113               482
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    82   2   6   8
  2Q GAIN WILD-TYPE 354   3  30  21
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              82               354
  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                          17    64
  2Q GAIN WILD-TYPE                        39   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                     17                39
  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    54  12
  3P GAIN WILD-TYPE 412  97
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               66               509 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12                97 
$`3P GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6782 
        5.26        37.02        16.04        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-A54L 
       41.00         1.58         1.02         0.20         0.95         5.19 
TCGA-AY-A69D TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-5868 TCGA-CM-6161 
        5.52        29.56         1.94         2.24        17.03        15.02 
TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6924 
       29.03        13.05        10.06        15.12        12.49        14.30 
TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6626 
       14.04         1.55        61.87        35.93        13.78        46.75 
TCGA-NH-A6GC TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3593 TCGA-AG-3612 TCGA-AG-3726 
        1.32        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        14.86         1.02 

$`3P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
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        15.52 
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-A6-6137 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-A6-6654 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        52.44         9.63         5.03         1.02         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-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-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-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-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.05         6.97        54.02         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
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-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-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-A00Q TCGA-AA-A00R 
       18.05        17.03         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 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A8YK TCGA-AZ-4308 
       15.75         0.20        21.44        17.82         6.87        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
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        48.20        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 
        8.02        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-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        11.08        11.08        11.01        12.03        14.99 
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-D5-6537 
       17.75        18.25         1.32         7.92        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         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-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        6.12        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-F4-6805 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         1.28         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 
       43.07        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-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       10.98        10.52         2.79         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        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         8.45 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        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         1.02         2.01        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-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-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-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         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-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
       36.03         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       60.03         7.99        11.01        15.02        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24        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-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-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-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.20              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            140.38 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            14.17             18.05 
[1] "0.2 - 129.3 (14.2)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    44  27
  3P GAIN WILD-TYPE 394 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     44   27
  3P GAIN WILD-TYPE  394  135
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON               44               394
  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      93        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         72         47       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                93
  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                72
  STAGE IIIC               6                47
  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  92 364  57
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                18
  T2              13                92
  T3              48               364
  T4               8                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 GAIN MUTATED    34  20  18
  3P GAIN WILD-TYPE 307 128  94
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              34               307
  N1              20               128
  N2              18                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  3P GAIN MUTATED    44   9   3   2  13
  3P GAIN WILD-TYPE 402  65   7   0  50
D5V7, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               44               402
  M1                9                65
  M1A               3                 7
  M1B               2                 0
  MX               13                50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    38  34
  3P GAIN WILD-TYPE 245 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   34
  3P GAIN WILD-TYPE  245  287
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              38               245
  MALE                34               287
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                     39                             5
  3P GAIN WILD-TYPE                  339                            54
                   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               339
  COLON MUCINOUS ADENOCARCINOMA                5                54
  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   8 524
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   71
  3P GAIN WILD-TYPE    8  524
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                1                 8
  YES              71               524
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    53   0   3   3
  3P GAIN WILD-TYPE 383   5  33  26
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              53               383
  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                        49   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                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(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    72  17
  3Q GAIN WILD-TYPE 394  92
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               89               486 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17                92 
$`3Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6137 
        5.26        37.02        16.04        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         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D 
        1.02         0.20        14.50         0.95         5.19         5.52 
TCGA-AZ-4614 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CM-4750 TCGA-CM-5868 
        5.65        29.56         1.94         2.24         8.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 
       15.02        14.04        29.03        13.05        10.06        15.12 
TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A285 TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6294 
       12.49        14.30         6.12        14.04         1.55        28.21 
TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC 
       61.87        39.42        35.93        13.78        46.75         1.32 
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        60.03        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        14.86         0.39         1.02         0.76 

$`3Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
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        15.52 
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-A6-5660 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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        22.52        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        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        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 
       29.95        23.01        20.98        13.94        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        14.93        17.03         0.99        33.07        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-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-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        50.99        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         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         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        31.00        38.07        35.01         1.02        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-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.43         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A8YK 
       16.31        15.75         0.20        21.44        17.82         6.87 
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-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
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        48.20        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-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        14.99        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-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
        1.32         7.92        17.85         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        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         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41        19.43       107.67         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        74.56        43.07        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        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 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        12.72        14.50         8.45        15.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         0.99        29.98         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-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04         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-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         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         4.60         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         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.00        13.97        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       30.05        10.06         5.29       126.44        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        37.51        31.30         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.46        18.28        55.76        47.08        26.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.20              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.08            140.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.500            18.265 
[1] "0.2 - 78.1 (14.5)"  "0.1 - 140.4 (18.3)"
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    62  34
  3Q GAIN WILD-TYPE 376 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     62   34
  3Q GAIN WILD-TYPE  376  128
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON               62               376
  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      91        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         67         44       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                91
  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                67
  STAGE IIIC               9                44
  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  90 345  55
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               4                16
  T2              15                90
  T3              67               345
  T4              10                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
  3Q GAIN MUTATED    44  30  22
  3Q GAIN WILD-TYPE 297 118  90
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              44               297
  N1              30               118
  N2              22                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  3Q GAIN MUTATED    60  13   4   2  17
  3Q GAIN WILD-TYPE 386  61   6   0  46
D6V7, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               60               386
  M1               13                61
  M1A               4                 6
  M1B               2                 0
  MX               17                46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    50  47
  3Q GAIN WILD-TYPE 233 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     50   47
  3Q GAIN WILD-TYPE  233  274
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              50               233
  MALE                47               274
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                     56                             6
  3Q GAIN WILD-TYPE                  322                            53
                   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               322
  COLON MUCINOUS ADENOCARCINOMA                6                53
  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   7 500
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   95
  3Q GAIN WILD-TYPE    7  500
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                2                 7
  YES              95               500
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    73   0   3   4
  3Q GAIN WILD-TYPE 363   5  33  25
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              73               363
  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                        47   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                47
  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 451 105
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               556 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               105 
$`4P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-A56B TCGA-AA-3560 TCGA-AA-3982 
        5.06        37.02        45.60        52.44        19.99        27.02 
TCGA-AD-A5EK TCGA-AY-A8YK TCGA-CM-5862 TCGA-G4-6307 TCGA-RU-A8FL TCGA-AG-3890 
        0.43         6.87         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-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-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         0.99         0.99 
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-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
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         0.99        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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.02         0.10         0.76         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-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         5.52        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        48.20        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         8.02        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        14.99 
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         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       61.87        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         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        67.00        24.13        17.95        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         8.45        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         1.02         2.01        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-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-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-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       20.98        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         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         4.60         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        60.03         7.99 
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-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        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-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        14.86         0.39         1.02 
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 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.43              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            55.04            140.38 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            19.99             17.77 
[1] "0.4 - 55.0 (20.0)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   9
  4P GAIN WILD-TYPE 427 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    9
  4P GAIN WILD-TYPE  427  153
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON               11               427
  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      98        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         74         52       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                98
  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                74
  STAGE IIIC               1                52
  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  20 100 397  65
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                20
  T2               5               100
  T3              15               397
  T4               0                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
  4P GAIN MUTATED    10   6   4
  4P GAIN WILD-TYPE 331 142 108
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              10               331
  N1               6               142
  N2               4               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  4P GAIN MUTATED    12   3   1   0   4
  4P GAIN WILD-TYPE 434  71   9   2  59
D7V7, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               12               434
  M1                3                71
  M1A               1                 9
  M1B               0                 2
  MX                4                59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  14
  4P GAIN WILD-TYPE 277 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   14
  4P GAIN WILD-TYPE  277  307
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               277
  MALE                14               307
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                     11                             0
  4P GAIN WILD-TYPE                  367                            59
                   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               367
  COLON MUCINOUS ADENOCARCINOMA                0                59
  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   9 575
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   20
  4P GAIN WILD-TYPE    9  575
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 9
  YES              20               575
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    17   0   0   0
  4P GAIN WILD-TYPE 419   5  36  29
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              17               419
  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                        51   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                51
  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 452 103
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               555 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               103 
$`4Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-5659 TCGA-A6-A56B 
       37.02        17.79        45.60        16.04        30.44        52.44 
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         0.43         6.87 
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-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        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-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         1.02         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-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-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-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         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        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-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        25.02        24.00        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         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 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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         1.58         1.02         0.10         0.76         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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
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        48.20 
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         8.02        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        14.99        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         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        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         1.28         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        43.07        61.87        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       26.99        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        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         8.45        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         1.02         2.01        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-3894 TCGA-AG-3896 
       19.99         1.02        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        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         4.60         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        60.03         7.99        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         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         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 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.43              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            55.04            140.38 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           25.525            17.690 
[1] "0.4 - 55.0 (25.5)"  "0.1 - 140.4 (17.7)"
[1] "hr=" "1.5"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   5
  4Q GAIN WILD-TYPE 422 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    5
  4Q GAIN WILD-TYPE  422  157
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON               16               422
  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      99        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         73         51       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                99
  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                73
  STAGE IIIC               2                51
  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  20 102 396  63
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                20
  T2               3               102
  T3              16               396
  T4               2                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
  4Q GAIN MUTATED     8   6   7
  4Q GAIN WILD-TYPE 333 142 105
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8               333
  N1               6               142
  N2               7               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  4Q GAIN MUTATED    13   6   0   0   2
  4Q GAIN WILD-TYPE 433  68  10   2  61
D8V7, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               13               433
  M1                6                68
  M1A               0                10
  M1B               0                 2
  MX                2                61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6  15
  4Q GAIN WILD-TYPE 277 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6   15
  4Q GAIN WILD-TYPE  277  306
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               6               277
  MALE                15               306
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                     16                             0
  4Q GAIN WILD-TYPE                  362                            59
                   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               362
  COLON MUCINOUS ADENOCARCINOMA                0                59
  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   9 574
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   21
  4Q GAIN WILD-TYPE    9  574
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 9
  YES              21               574
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    16   0   2   0
  4Q GAIN WILD-TYPE 420   5  34  29
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              16               420
  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                        52   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                52
  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 386  90
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               99               476 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                90 
$`5P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
        5.06        44.91        45.60        37.25        16.04        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         0.99 
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         1.58 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6603 
        0.43         0.92         0.20         6.87        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         8.02        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         1.32         6.64        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         1.02        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        14.86 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
        1.02         0.53         0.76 

$`5P GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.26        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        13.94        15.52        37.05 
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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        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        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01         0.99        14.01        33.99        21.01        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-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 
       50.04        47.05        15.02        11.01        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       36.95        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        53.00        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-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-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        17.03         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         0.99        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-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        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-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 
        1.02         0.10         0.76         0.20         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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        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        48.20        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        14.99 
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         7.92        15.12        17.85         4.50        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         1.28         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        43.07        61.87        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       17.29        14.76        67.00        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
        8.45        15.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        8.02         7.07         2.01        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-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-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        19.99        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        15.95         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 
       64.01        10.98        51.98        49.97        61.97         0.49 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         4.60         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-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.00        13.97        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         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-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-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         8.45        37.51        31.30         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         1.12         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            98.24            140.38 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            14.99             18.15 
[1] "0.2 - 98.2 (15.0)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    67  36
  5P GAIN WILD-TYPE 371 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     67   36
  5P GAIN WILD-TYPE  371  126
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON               67               371
  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      90        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         65         37       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                90
  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                65
  STAGE IIIC              16                37
  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  85 343  52
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                19
  T2              20                85
  T3              69               343
  T4              13                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
  5P GAIN MUTATED    45  31  26
  5P GAIN WILD-TYPE 296 117  86
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               296
  N1              31               117
  N2              26                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  5P GAIN MUTATED    70  14   3   1  11
  5P GAIN WILD-TYPE 376  60   7   1  52
D9V7, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               70               376
  M1               14                60
  M1A               3                 7
  M1B               1                 1
  MX               11                52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    48  55
  5P GAIN WILD-TYPE 235 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     48   55
  5P GAIN WILD-TYPE  235  266
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              48               235
  MALE                55               266
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                     59                             8
  5P GAIN WILD-TYPE                  319                            51
                   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               319
  COLON MUCINOUS ADENOCARCINOMA                8                51
  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   6 495
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  100
  5P GAIN WILD-TYPE    6  495
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3                 6
  YES             100               495
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    76   1   9   2
  5P GAIN WILD-TYPE 360   4  27  27
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              76               360
  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                        42   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                42
  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    50  12
  5Q GAIN WILD-TYPE 416  97
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               62               513 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                97 
$`5Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
        5.06        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         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3939 TCGA-AA-3968 TCGA-AA-3976 
       14.93         0.99        17.03        12.99        21.99        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 
       51.98         2.96        40.96         1.58         0.43        15.75 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 
       49.41        29.56        11.74        13.02        16.01        15.02 
TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-DM-A1D8 TCGA-DM-A28M 
       14.99        11.01        19.59        17.75        12.59        95.18 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-AF-6655 TCGA-AF-6672 
       46.75        47.15         1.32         6.64        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-4007 
       65.98         1.02        19.99         1.02        17.03         1.02 
TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 
       25.97        12.00        31.00        41.00        38.04         0.69 
TCGA-AH-6644 TCGA-DC-6683 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 
        0.72        10.06        16.31        11.51        11.97         9.96 
TCGA-F5-6811 TCGA-F5-6814 
        1.02         0.53 

$`5Q GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.26        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        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-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-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04         0.99 
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-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       38.99        36.95        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-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        17.03 
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         0.99        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         1.02         0.10         0.76         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
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-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        48.20        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-5341 
       37.02         8.02        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-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         1.28         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        43.07        61.87        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-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.17        91.79        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       17.29        14.76        30.28        67.00        24.13        17.95 
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-A56K TCGA-AF-A56N 
       10.39        14.50         8.45        15.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
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-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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       19.99        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        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-A01W 
       37.02        15.95        36.03         9.07         1.02        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-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.97         0.49         1.45         4.60         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 
       60.03         7.99        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         7.10        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-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-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46         8.45        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.43              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            95.18            140.38 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.385            18.050 
[1] "0.4 - 95.2 (15.4)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    41  24
  5Q GAIN WILD-TYPE 397 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     41   24
  5Q GAIN WILD-TYPE  397  138
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON               41               397
  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         9        0        3        16         1         1
  5Q GAIN WILD-TYPE      93        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         72         45       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                  9                93
  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                72
  STAGE IIIC               8                45
  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  15  42   8
  5Q GAIN WILD-TYPE  20  90 370  57
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                20
  T2              15                90
  T3              42               370
  T4               8                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
  5Q GAIN MUTATED    31  20  13
  5Q GAIN WILD-TYPE 310 128  99
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              31               310
  N1              20               128
  N2              13                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5Q GAIN MUTATED    45   9   1   1   7
  5Q GAIN WILD-TYPE 401  65   9   1  56
D10V7, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               45               401
  M1                9                65
  M1A               1                 9
  M1B               1                 1
  MX                7                56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    30  35
  5Q GAIN WILD-TYPE 253 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     30   35
  5Q GAIN WILD-TYPE  253  286
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              30               253
  MALE                35               286
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                     37                             4
  5Q GAIN WILD-TYPE                  341                            55
                   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                        37               341
  COLON MUCINOUS ADENOCARCINOMA                4                55
  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  64
  5Q GAIN WILD-TYPE   8 531
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   64
  5Q GAIN WILD-TYPE    8  531
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                 8
  YES              64               531
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    48   0   6   1
  5Q GAIN WILD-TYPE 388   5  30  28
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              48               388
  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                        46   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                46
  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    95  19
  6P GAIN WILD-TYPE 371  90
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              114               461 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19                90 
$`6P GAIN MUTATED`
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       43.43        23.38        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        52.44        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         0.99        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         1.02        14.50 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 
        0.95         0.20         5.19        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-RU-A8FL 
       39.42        91.79        46.75        10.98         1.32        30.28 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       24.13        43.04        37.74        10.39        14.50        15.39 
TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 
       65.98        46.03        19.99        29.98         1.02         1.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       14.04         1.02         0.99        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 
       31.00         0.72        10.19         6.05         9.37        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6511 
       12.00        15.02        36.00       129.27        20.55        15.85 
TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 TCGA-G5-6641 
       17.69        37.51        14.86         0.39        18.28        26.43 

$`6P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        43.76        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        34.65        14.53        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04         0.99         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 
       17.98        15.95        38.99        36.95        14.93         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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-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-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       26.01        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        17.03 
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         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        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-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-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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         1.58         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09        16.31        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.52         6.87        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        48.20 
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         8.02        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        14.99        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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        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 
        1.28         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        43.07        61.87        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         4.11        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       14.76        67.00        17.95        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         8.45        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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        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         4.60         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        60.03         7.99        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         7.10        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         1.02         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 
             0.20              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            140.38 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            17.41             17.85 
[1] "0.2 - 129.3 (17.4)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    81  39
  6P GAIN WILD-TYPE 357 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     81   39
  6P GAIN WILD-TYPE  357  123
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON               81               357
  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        17        0        3        24         2         1
  6P GAIN WILD-TYPE      85        1       33       147         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           6          7         21         14       15
  6P GAIN WILD-TYPE        20         14         57         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                 17                85
  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                57
  STAGE IIIC              14                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  17  85  14
  6P GAIN WILD-TYPE  14  88 327  51
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6                14
  T2              17                88
  T3              85               327
  T4              14                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
  6P GAIN MUTATED    53  31  37
  6P GAIN WILD-TYPE 288 117  75
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              53               288
  N1              31               117
  N2              37                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  6P GAIN MUTATED    83  19   4   1  11
  6P GAIN WILD-TYPE 363  55   6   1  52
D11V7, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               83               363
  M1               19                55
  M1A               4                 6
  M1B               1                 1
  MX               11                52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    51  71
  6P GAIN WILD-TYPE 232 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     51   71
  6P GAIN WILD-TYPE  232  250
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              51               232
  MALE                71               250
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                     72                             9
  6P GAIN WILD-TYPE                  306                            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                        72               306
  COLON MUCINOUS ADENOCARCINOMA                9                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     7 115
  6P GAIN WILD-TYPE   2 480
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7  115
  6P GAIN WILD-TYPE    2  480
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                7                 2
  YES             115               480
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    90   0  11   4
  6P GAIN WILD-TYPE 346   5  25  25
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              90               346
  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                          13    63
  6P GAIN WILD-TYPE                        43   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                     13                43
  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    85  16
  6Q GAIN WILD-TYPE 381  93
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              101               474 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                93 
$`6Q GAIN MUTATED`
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6142 
       43.43        23.38        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         0.99        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         1.02        14.50 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 
        0.95         0.20         5.19         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-RU-A8FL TCGA-AF-2687 TCGA-AF-3911 
       91.79        10.98         1.32        30.28        24.13        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3612 TCGA-AG-3728 
       10.39        14.50        15.39        65.98        19.99        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 
        1.02         1.02         1.02         0.99        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
       12.00        31.00         0.72        10.19         6.05         9.37 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6506 
       12.99        12.00        15.02        36.00        51.48        20.55 
TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       15.85        17.69        37.51        14.86         0.39 

$`6Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        43.76        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       36.95        14.93         0.99        33.07        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-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        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-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
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         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        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-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-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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         1.58         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09        16.31        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.52         6.87        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        48.20        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         8.02        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        14.99        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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        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         1.28         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        43.07        61.87 
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         4.11        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        14.76        67.00        17.95        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         8.45        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         1.02         2.01        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         4.60         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        60.03         7.99        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         7.10        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         1.02         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 
             0.20              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           117.07            140.38 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           15.850            18.015 
[1] "0.2 - 117.1 (15.8)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    73  34
  6Q GAIN WILD-TYPE 365 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     73   34
  6Q GAIN WILD-TYPE  365  128
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON               73               365
  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        15        0        3        20         2         0
  6Q GAIN WILD-TYPE      87        1       33       151         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           6          6         18         12       13
  6Q GAIN WILD-TYPE        20         15         60         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                 15                87
  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                60
  STAGE IIIC              12                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  16  74  15
  6Q GAIN WILD-TYPE  16  89 338  50
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                16
  T2              16                89
  T3              74               338
  T4              15                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
  6Q GAIN MUTATED    47  29  32
  6Q GAIN WILD-TYPE 294 119  80
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              47               294
  N1              29               119
  N2              32                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  6Q GAIN MUTATED    72  19   4   1   9
  6Q GAIN WILD-TYPE 374  55   6   1  54
D12V7, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               72               374
  M1               19                55
  M1A               4                 6
  M1B               1                 1
  MX                9                54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    47  62
  6Q GAIN WILD-TYPE 236 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     47   62
  6Q GAIN WILD-TYPE  236  259
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              47               236
  MALE                62               259
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                     66                             7
  6Q GAIN WILD-TYPE                  312                            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                        66               312
  COLON MUCINOUS ADENOCARCINOMA                7                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     7 102
  6Q GAIN WILD-TYPE   2 493
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  102
  6Q GAIN WILD-TYPE    2  493
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                 2
  YES             102               493
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    80   0  10   4
  6Q GAIN WILD-TYPE 356   5  26  25
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              80               356
  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                          12    57
  6Q GAIN WILD-TYPE                        44   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                     12                44
  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  64
  7P GAIN WILD-TYPE 202  45
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              328               247 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64                45 
$`7P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        5.06         5.26        37.02        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       29.16        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       20.61        24.69        23.87        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01        58.03         6.97        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       36.03        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       13.02        24.00        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 
        6.05        54.02         2.01        14.01        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-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        0.99        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 
       29.98        18.05        31.00        24.00        24.00        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3994 
       21.99        16.08        34.06        26.01        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A017 
       13.94        19.00        34.03        17.03        42.02        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H 
       15.02        32.02        33.04        26.01        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
        5.03         0.92        39.98        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         1.58         1.02         0.10         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-4682 
        5.19         6.87        75.25        50.37        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        61.41        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23         3.19         1.94         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
        3.29         1.35        17.56       102.44        40.34        21.99 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        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-6167 
       17.03        15.02        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       12.99        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
       10.06        19.59        11.51        17.75         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       15.12         4.50        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       38.20        92.75        49.91        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
      131.51         7.76         6.12        14.04        35.97       117.07 
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-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
        0.53        35.41       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       74.56        61.87        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 
       35.93        36.72        36.00        26.43        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        47.15         4.11         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        5.19         6.64        30.28        67.00        24.13        17.95 
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       17.23        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       20.02        86.63        65.98         7.07         1.02        24.00 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       46.03        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 
       19.99        29.98         0.99         0.99        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 
       35.01         1.02        48.03        19.99        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       17.03         0.99        25.97        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G 
        1.02        12.00        31.00        70.03         1.94        38.96 
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         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         9.37         4.73        60.03         7.99        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         7.10 
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-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 
      129.27        24.13         0.49         2.40        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         8.45         9.96        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39         1.02         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 

$`7P GAIN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        17.79        42.28        15.52        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         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       17.98        15.95        38.99        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       36.03        31.07        53.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 
       26.01         2.01        34.03         2.01        50.99        13.05 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        24.00        19.07         7.96        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        21.99        34.98         0.99        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-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W 
       37.02        39.06         2.96        39.98        22.03        41.00 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
       18.05         0.07        56.55         0.72         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4323 
        0.92        27.09        21.44         5.52        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
        5.65        32.94         5.13         6.77       100.01        11.74 
TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
        2.24         0.07         0.26         0.33         0.10        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        48.20        51.32        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        21.99        13.02        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        14.99        12.26        13.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       18.25        17.85        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 
       11.64         1.51        12.00        11.38       119.70       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
       13.32       140.38       135.65       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
      119.93        60.79        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         1.28        19.43 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 
        8.35        43.07        53.62        51.75        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        52.80        10.98        10.52         2.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 
        5.49        26.99        17.29        14.76        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       19.10        12.72        10.39        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
       32.02         8.02         2.01         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 
       50.04         7.99         0.99         1.02        32.98         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95        13.02        14.01        32.02        28.04        14.04 
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-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98        49.97        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 
        1.81         6.05         6.97        13.97        15.02        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       30.05        12.95        51.48        32.61        20.55        19.96 
TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 
       17.00        16.41         8.61        17.46        37.51         0.53 
TCGA-F5-6861 
        1.12 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           131.51            140.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            17.03             18.25 
[1] "0.1 - 131.5 (17.0)" "0.1 - 140.4 (18.2)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   241 102
  7P GAIN WILD-TYPE 197  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    241  102
  7P GAIN WILD-TYPE  197   60
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON              241               197
  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        56        1       18        74         3         2
  7P GAIN WILD-TYPE      46        0       18        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          13         15         56         37       41
  7P GAIN WILD-TYPE        13          6         22         16       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                 56                46
  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              56                22
  STAGE IIIC              37                16
  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  60 233  37
  7P GAIN WILD-TYPE   7  45 179  28
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              13                 7
  T2              60                45
  T3             233               179
  T4              37                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   166 101  75
  7P GAIN WILD-TYPE 175  47  37
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             166               175
  N1             101                47
  N2              75                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  7P GAIN MUTATED   241  49   8   1  40
  7P GAIN WILD-TYPE 205  25   2   1  23
D13V7, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              241               205
  M1               49                25
  M1A               8                 2
  M1B               1                 1
  MX               40                23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   159 186
  7P GAIN WILD-TYPE 124 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    159  186
  7P GAIN WILD-TYPE  124  135
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             159               124
  MALE               186               135
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                    216                            25
  7P GAIN WILD-TYPE                  162                            34
                   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                       216               162
  COLON MUCINOUS ADENOCARCINOMA               25                34
  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     7 338
  7P GAIN WILD-TYPE   2 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7  338
  7P GAIN WILD-TYPE    2  257
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                7                 2
  YES             338               257
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   248   4  24  14
  7P GAIN WILD-TYPE 188   1  12  15
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             248               188
  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                          38   176
  7P GAIN WILD-TYPE                        18   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                     38                18
  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   240  55
  7Q GAIN WILD-TYPE 226  54
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              295               280 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               55                54 
$`7Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
        5.06         5.26        37.02        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        16.04        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         1.02 
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-3855 
       35.05         0.99        36.95        37.02        14.93        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       31.00        24.00        24.00         2.01        20.98        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         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.43         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         5.19         6.87        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         8.02 
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         7.92        15.12         4.50        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 
       61.87        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         4.11         5.98         5.59         1.32         5.19 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 
        6.64        30.28        67.00        24.13        17.95        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       14.50         8.45        15.39        20.02        86.63        65.98 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        7.07         1.02        24.00        46.03        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99        19.99        29.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       19.99        17.03        35.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       28.04         1.02         0.99        25.97        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A02G 
        9.07         1.02        12.00        31.00        70.03        38.96 
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         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.05         9.37        60.03         7.99        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.99        12.00        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
       10.06         5.29        41.36        57.24        24.13         0.49 
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-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.51        11.97         9.96        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.02         0.69         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`7Q GAIN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        23.38        17.79        42.28        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 
       37.05        34.65        36.53        14.53        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 
       22.09        22.06        32.71        27.09         8.38        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3492 
       24.39        20.12        19.66        61.84        52.44         3.02 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 
        8.05        19.07        19.07        34.03        29.00         0.99 
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-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         0.92        50.04        47.05        47.01 
TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 
       19.00        26.99        19.04         0.99         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3848 
        1.02        17.98        15.95        38.99        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 
       33.07        36.03        31.07        53.00        17.03         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 
       12.99        33.01        26.01        34.03         2.01        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       13.05        26.01        25.02        24.00        19.07         7.96 
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        17.03         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-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        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-A02E 
       35.01         1.02        35.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       39.98        22.03        41.00        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72         1.58         0.76         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       15.75        21.44         5.52        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        48.20        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        14.99        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         1.28        19.43 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       28.21         8.35        43.07        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        10.52 
TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2690 
        2.79         5.49        26.99        17.29        14.76        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         8.02         2.01 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 
        1.02        34.03         2.01        50.04         6.05         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-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       14.01        32.02        36.03        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 
       13.94         6.02        23.01        37.02        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       51.98        49.97         1.94        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 
        1.81         6.05         6.97         4.73        13.97        15.02 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
       13.97        30.05        12.95       126.44       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 
       32.61         2.40        20.55        19.96        17.00        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-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
        0.66         0.53         1.12        18.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           131.51            140.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            16.31             18.64 
[1] "0.1 - 131.5 (16.3)" "0.1 - 140.4 (18.6)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   221  86
  7Q GAIN WILD-TYPE 217  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    221   86
  7Q GAIN WILD-TYPE  217   76
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON              221               217
  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        53        1       16        63         3         1
  7Q GAIN WILD-TYPE      49        0       20       108         7         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          12         10         54         32       37
  7Q GAIN WILD-TYPE        14         11         24         21       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                 53                49
  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              54                24
  STAGE IIIC              32                21
  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  52 205  31
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              13                 7
  T2              53                52
  T3             207               205
  T4              34                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
  7Q GAIN MUTATED   150  89  67
  7Q GAIN WILD-TYPE 191  59  45
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             150               191
  N1              89                59
  N2              67                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  7Q GAIN MUTATED   212  45   8   1  37
  7Q GAIN WILD-TYPE 234  29   2   1  26
D14V7, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              212               234
  M1               45                29
  M1A               8                 2
  M1B               1                 1
  MX               37                26
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   142 167
  7Q GAIN WILD-TYPE 141 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    142  167
  7Q GAIN WILD-TYPE  141  154
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             142               141
  MALE               167               154
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                    198                            23
  7Q GAIN WILD-TYPE                  180                            36
                   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               180
  COLON MUCINOUS ADENOCARCINOMA               23                36
  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   4 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  304
  7Q GAIN WILD-TYPE    4  291
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                5                 4
  YES             304               291
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   223   3  23  14
  7Q GAIN WILD-TYPE 213   2  13  15
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             223               213
  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                          36   154
  7Q GAIN WILD-TYPE                        20   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                     36                20
  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   124  32
  8P GAIN WILD-TYPE 342  77
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              156               419 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                77 
$`8P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4107 
        5.06         5.26        17.79        13.94        16.04        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         0.99 
TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
        0.99        17.03        31.07        29.98        18.05        12.99 
TCGA-AA-3966 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A029 
        2.01        18.05         0.99        17.03         0.99        51.98 
TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 
        2.96         5.03         0.92         0.07         1.58         0.10 
TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4615 
        0.43        27.09        21.44         5.19         6.87        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 
        5.13        22.36        65.00        61.41        49.41         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-4948 
        3.19         2.24         3.06         2.14         0.07       102.44 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         2.01        20.02        37.02         8.02         8.02 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       27.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6529 
       29.03        14.99        12.99        11.08        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
       17.75         1.32         4.50        17.13        16.14         7.53 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43        14.30        10.26       119.70        24.43        38.20 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        7.50        44.32        35.97       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 
       13.45         6.18        16.24         8.35        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6626 TCGA-G4-6627 
       53.62        44.68        45.11        39.42        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-WS-AB45 TCGA-AF-2691 
        4.11         5.59        17.29         6.64        67.00        43.04 
TCGA-AF-3400 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3598 
       12.72        20.02        65.98        36.03        32.02        50.04 
TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 
        1.02        36.95         1.02        48.03        32.02         1.02 
TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A032 
        0.99         9.07        31.00        70.03        64.01        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-6156 
        0.49         0.69         6.05         9.37         7.99        15.02 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 
       13.05        41.36        57.24        24.13         0.49        17.00 
TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6572 
       16.31        11.51        37.51         0.39         0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       37.02        46.65        43.76        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 
       34.65        36.53        14.53        32.91        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        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-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        52.44         5.03         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 
       37.05         1.02        58.03        63.98        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       34.03        26.01         0.99        33.99        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-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 
       19.99        61.02        78.08        54.02         2.01         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-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       19.00        36.00        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 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-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-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       42.02        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-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.06        39.98         2.01        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.02         0.76         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       83.80        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       11.74         1.94         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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       16.01         5.03        12.00        14.04        16.04        21.99 
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        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       19.59        13.51        20.42        18.25         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
       17.85        12.49        15.58        12.39        10.13         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-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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 
       26.47        81.37       119.93        60.79        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64        35.87         1.55        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6309 
       28.21        82.39        23.51        74.56        55.04        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-G4-6628 TCGA-NH-A50U 
       13.78        35.80        26.17        91.79        52.80        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       26.99        14.76        30.28        24.13        17.95        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         8.45 
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         1.02         2.01        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         4.60         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        60.03        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         7.10 
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        14.86         1.02         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 
             0.07              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           119.70            140.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            16.09             19.00 
[1] "0.1 - 119.7 (16.1)" "0.1 - 140.4 (19.0)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   127  40
  8P GAIN WILD-TYPE 311 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    127   40
  8P GAIN WILD-TYPE  311  122
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON              127               311
  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      74        1       22       124         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           4          3         22         15       20
  8P GAIN WILD-TYPE        22         18         56         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                74
  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                56
  STAGE IIIC              15                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  27 117  17
  8P GAIN WILD-TYPE  15  78 295  48
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               5                15
  T2              27                78
  T3             117               295
  T4              17                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
  8P GAIN MUTATED   101  34  31
  8P GAIN WILD-TYPE 240 114  81
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             101               240
  N1              34               114
  N2              31                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  8P GAIN MUTATED   119  24   3   0  19
  8P GAIN WILD-TYPE 327  50   7   2  44
D15V7, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              119               327
  M1               24                50
  M1A               3                 7
  M1B               0                 2
  MX               19                44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    79  88
  8P GAIN WILD-TYPE 204 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     79   88
  8P GAIN WILD-TYPE  204  233
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              79               204
  MALE                88               233
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                    113                            14
  8P GAIN WILD-TYPE                  265                            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               265
  COLON MUCINOUS ADENOCARCINOMA               14                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     3 164
  8P GAIN WILD-TYPE   6 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3  164
  8P GAIN WILD-TYPE    6  431
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                3                 6
  YES             164               431
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   111   0  14  12
  8P GAIN WILD-TYPE 325   5  22  17
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             111               325
  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                          17    90
  8P GAIN WILD-TYPE                        39   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                     17                39
  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  58
  8Q GAIN WILD-TYPE 232  51
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              292               283 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               58                51 
$`8Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 
        5.06         5.26        43.43        17.79        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        16.04        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-3532 TCGA-AA-3534 
        6.97         1.02        36.03        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       23.01        20.98        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       37.05        36.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       36.95        37.02        17.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       34.03         2.01        16.08        34.06        26.01        24.00 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       13.94        19.00        18.05         0.99        17.03         0.99 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       12.00        31.00         1.02        37.02        51.98         2.96 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 
        5.03         0.92        41.00         0.07         4.21         1.58 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
        0.10         0.43         0.92        27.09        16.31        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
        5.19         6.87        75.25        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        61.41        49.41        12.10        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-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
        2.14         0.07         0.10         1.35       102.44        15.62 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         2.01        20.02        37.02         8.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       27.02        13.02        29.06        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 
        5.03        15.02        15.02        17.03        15.02        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5540 
       21.99        14.99        12.99        13.02        11.08        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.19        17.75         1.32         7.92        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        4.50        17.13        16.14        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA 
      119.70        24.43        38.20       130.65       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       44.32         6.12        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        13.38        13.64        13.45         6.18        16.31 
TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       16.24         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.43        46.75        47.15         4.11        10.98 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
        5.98         5.59         5.49        17.29         6.64        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       12.72        37.74        10.39        20.02        10.39        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02         1.02        24.00         1.02        46.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 
       50.04         6.05         0.99        19.99         7.99         1.02 
TCGA-AG-3732 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       32.98        36.95         1.02        48.03        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A011 
       14.04         1.02        17.03         0.99        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       51.98         1.94        38.04         0.49         1.45         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.05         9.37         4.73        60.03         7.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97        15.02         7.10        13.05        10.06 
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-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.00        16.34        16.31        11.51        10.78        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        9.96        37.51        14.86         0.39         1.02         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

$`8Q GAIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 
       15.52        37.05        34.65        14.53        30.44        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       22.09        22.06        22.52         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       61.84        52.44         1.02         3.02        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 
       29.95        19.99        13.94        61.02         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       47.05        11.01        19.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       14.93         0.99        33.07        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
        2.01        20.98        21.99        50.99        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       27.02        19.07         7.96        27.02        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y 
       26.01        39.06        39.98         2.01        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 
        1.02         0.76         0.20         0.46        14.50         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 
       15.75         0.20        17.82         5.52        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 
        1.41         5.65        62.79         6.77       100.01         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        3.29         0.26         0.33        17.56        40.34        70.16 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       26.04        22.03        16.01        12.00        14.04        16.04 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 
       20.42        18.25        17.85        12.49        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.64         1.51        12.00        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       12.59       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 
       26.47        81.37       119.93        95.18        11.11        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        29.59        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 
       19.43       107.67        28.21        82.39        51.75        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-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
       52.80        10.52         2.79         1.32         5.19        26.99 
TCGA-QG-A5Z2 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       14.76        19.10        14.50         8.45        15.39        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 
       11.84        12.00         8.02         7.07         2.01        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
        2.01        12.03        15.95        19.99         0.99        29.98 
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-4001 TCGA-AG-A002 TCGA-AG-A008 
       35.01        14.01        19.99        36.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        36.03        12.00        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        41.00         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.05         6.97        13.97        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        36.00        30.05        12.95         5.29       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 
       15.85        17.69        16.41         8.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        8.45        31.30         0.66         0.69         0.53         1.12 
TCGA-G5-6233 
       18.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.20 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           140.38            139.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           17.015            19.070 
[1] "0.1 - 140.4 (17.0)" "0.2 - 139.2 (19.1)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   222  87
  8Q GAIN WILD-TYPE 216  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    222   87
  8Q GAIN WILD-TYPE  216   75
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON              222               216
  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      57        1       15        87         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          11         13         39         32       42
  8Q GAIN WILD-TYPE        15          8         39         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                57
  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                39
  STAGE IIIC              32                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  53 218  32
  8Q GAIN WILD-TYPE  14  52 194  33
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               6                14
  T2              53                52
  T3             218               194
  T4              32                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8Q GAIN MUTATED   166  74  68
  8Q GAIN WILD-TYPE 175  74  44
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             166               175
  N1              74                74
  N2              68                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  8Q GAIN MUTATED   219  48   7   0  33
  8Q GAIN WILD-TYPE 227  26   3   2  30
D16V7, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              219               227
  M1               48                26
  M1A               7                 3
  M1B               0                 2
  MX               33                30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   144 166
  8Q GAIN WILD-TYPE 139 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    144  166
  8Q GAIN WILD-TYPE  139  155
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             144               139
  MALE               166               155
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                    199                            22
  8Q GAIN WILD-TYPE                  179                            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               179
  COLON MUCINOUS ADENOCARCINOMA               22                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     8 302
  8Q GAIN WILD-TYPE   1 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8  302
  8Q GAIN WILD-TYPE    1  293
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                8                 1
  YES             302               293
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   211   3  26  17
  8Q GAIN WILD-TYPE 225   2  10  12
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             211               225
  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                          31   157
  8Q GAIN WILD-TYPE                        25   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                     31                25
  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  30
  9P GAIN WILD-TYPE 385  79
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              111               464 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               30                79 
$`9P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-6142 
       37.02        44.91        13.94        16.04        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        52.44         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-3854 TCGA-AA-3856 
        2.01        50.04        14.93         0.99        36.03         0.99 
TCGA-AA-3869 TCGA-AA-3976 TCGA-AA-3994 TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C 
       27.02        26.01        27.02        42.02        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-5543 
        0.99        51.98         1.58         1.02         0.43        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5796 
        0.20         5.19        50.37        12.10        29.56         3.25 
TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       21.99        13.02        22.03         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6539 
       14.04        29.03        14.99        19.59        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-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       26.47        98.24        95.18         8.61        13.38         6.18 
TCGA-F4-6704 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC 
        1.55        13.78        91.79        46.75        10.98         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 
        5.19        26.99        67.00        17.95        17.23        12.72 
TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3612 
       20.02        46.03         2.01        50.04         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-4001 
        7.99         0.99        17.03         1.02        32.02        36.03 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 
       70.03        10.98        51.98        38.04         0.69         0.72 
TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 
       10.98        36.00       129.27         2.40        11.51        10.78 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 
        8.45         9.96        14.86         0.39         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`9P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        45.60        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 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-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       23.87        20.12        19.66        24.92        61.84         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 
       19.07        34.03        26.01        12.99         0.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 
       13.94        19.99        61.02         6.05        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       17.03        33.07        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
       33.04        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82         5.52         6.87        75.25        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-6601 
       65.00        62.79        61.41        49.41         6.77       100.01 
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-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       48.20        51.32        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         8.02        26.04         8.02 
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-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       15.02        15.02        12.00        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
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         7.92        15.12        17.85         4.50        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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 
      117.07        11.11        13.64        13.45        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         1.28         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        43.07        61.87        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-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       26.43        22.09        26.04        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11        10.52         2.79         5.98         5.59 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 
        5.49        17.29         6.64        14.76        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 
        8.45        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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 
        2.01        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         4.60         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        60.03         7.99        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         7.10        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         1.02         0.66         0.53         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.20              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            140.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           15.020            18.265 
[1] "0.2 - 129.3 (15.0)" "0.1 - 140.4 (18.3)"
[1] "hr=" "1.8"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    78  42
  9P GAIN WILD-TYPE 360 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     78   42
  9P GAIN WILD-TYPE  360  120
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON               78               360
  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        14        1        7        31         2         2
  9P GAIN WILD-TYPE      88        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         67         35       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                 14                88
  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                67
  STAGE IIIC              18                35
  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  16  84  16
  9P GAIN WILD-TYPE  17  89 328  49
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               3                17
  T2              16                89
  T3              84               328
  T4              16                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
  9P GAIN MUTATED    60  31  28
  9P GAIN WILD-TYPE 281 117  84
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              60               281
  N1              31               117
  N2              28                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  9P GAIN MUTATED    85  13   4   1  14
  9P GAIN WILD-TYPE 361  61   6   1  49
D17V7, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               85               361
  M1               13                61
  M1A               4                 6
  M1B               1                 1
  MX               14                49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    58  62
  9P GAIN WILD-TYPE 225 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     58   62
  9P GAIN WILD-TYPE  225  259
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              58               225
  MALE                62               259
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                     60                            18
  9P GAIN WILD-TYPE                  318                            41
                   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                        60               318
  COLON MUCINOUS ADENOCARCINOMA               18                41
  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     1 119
  9P GAIN WILD-TYPE   8 476
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1  119
  9P GAIN WILD-TYPE    8  476
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 8
  YES             119               476
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    94   0   6   3
  9P GAIN WILD-TYPE 342   5  30  26
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              94               342
  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                          16    55
  9P GAIN WILD-TYPE                        40   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                     16                40
  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    67  26
  9Q GAIN WILD-TYPE 399  83
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               93               482 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26                83 
$`9Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-A565 
       37.02        44.91        13.94        16.04        31.63        16.24 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
       52.44         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-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 
        0.99        36.03         0.99        27.02        27.02        13.94 
TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 
       42.02        21.99        15.02         0.99        51.98         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4313 
        1.02         0.43        15.75         0.20         5.19        50.37 
TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-5864 
       12.10         3.25        21.99        13.02         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-WS-AB45 
       91.79        46.75        10.98         1.32         5.19        67.00 
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       17.95        12.72        20.02         2.01        50.04         0.99 
TCGA-AG-3878 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 TCGA-AG-A023 
        0.99        17.03         1.02        32.02        10.98        51.98 
TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 
       38.04         0.72        10.98        36.00       129.27         2.40 
TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 
       11.51        10.78         9.96         0.39         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`9Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        45.60        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        32.91 
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-A566 
       24.39        23.87        20.12        19.66        20.28        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3538 
       36.03         8.05        19.07        19.07        34.03        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        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-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.05        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         0.99         0.99 
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-3846 TCGA-AA-3851 TCGA-AA-3855 
       38.99        36.95        37.02        17.03        33.07        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-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-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         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         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        6.87        75.25        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-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-5797 
        3.19         1.94         2.24         3.06         2.14         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        48.20        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-4750 TCGA-CM-4751 TCGA-CM-5341 
       37.02         8.02        26.04         8.02        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        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        14.99        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         7.92        15.12        17.85         4.50        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         1.28 
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        43.07        61.87        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         4.11        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.98         5.59         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       14.76        30.28        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
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         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
        1.02        46.03        34.03        12.03         6.05        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-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-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-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-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         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        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-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-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        8.61        13.64        17.46        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
       31.30        14.86         1.02         0.66         0.53         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.20              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            140.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            14.04             19.02 
[1] "0.2 - 129.3 (14.0)" "0.1 - 140.4 (19.0)"
[1] "hr=" "1.8"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    69  32
  9Q GAIN WILD-TYPE 369 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     69   32
  9Q GAIN WILD-TYPE  369  130
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON               69               369
  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        12        1        5        30         1         2
  9Q GAIN WILD-TYPE      90        0       31       141         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         70         39       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                 12                90
  STAGE IA                 1                 0
  STAGE II                 5                31
  STAGE IIA               30               141
  STAGE IIB                1                 9
  STAGE IIC                2                 1
  STAGE III                3                23
  STAGE IIIA               6                15
  STAGE IIIB               8                70
  STAGE IIIC              14                39
  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  12  72  13
  9Q GAIN WILD-TYPE  17  93 340  52
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               3                17
  T2              12                93
  T3              72               340
  T4              13                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
  9Q GAIN MUTATED    54  23  23
  9Q GAIN WILD-TYPE 287 125  89
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              54               287
  N1              23               125
  N2              23                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  9Q GAIN MUTATED    72  12   3   1  10
  9Q GAIN WILD-TYPE 374  62   7   1  53
D18V7, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               72               374
  M1               12                62
  M1A               3                 7
  M1B               1                 1
  MX               10                53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    45  56
  9Q GAIN WILD-TYPE 238 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     45   56
  9Q GAIN WILD-TYPE  238  265
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              45               238
  MALE                56               265
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                     53                            16
  9Q GAIN WILD-TYPE                  325                            43
                   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               325
  COLON MUCINOUS ADENOCARCINOMA               16                43
  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   8 495
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1  100
  9Q GAIN WILD-TYPE    8  495
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 8
  YES             100               495
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    78   0   6   3
  9Q GAIN WILD-TYPE 358   5  30  26
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              78               358
  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                        41   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                41
  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    29  12
  10P GAIN WILD-TYPE 437  97
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                41                534 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 97 
$`10P GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6650 
        5.26        37.02        16.04        32.45        24.16        20.61 
TCGA-A6-6782 TCGA-AA-3548 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3952 
       20.28        33.99         2.01        33.07        27.02         2.01 
TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-5862 
       16.31         5.19         6.87         2.24        16.01         5.03 
TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6924 
       14.04        11.01        19.59        13.51         7.92        14.30 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 
       12.59         7.50         8.61         1.55        74.56        36.00 
TCGA-G4-6625 TCGA-AF-2689 TCGA-AG-3902 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W 
       91.79        17.95        32.02        15.95         9.07        70.03 
TCGA-BM-6198 TCGA-DC-4745 TCGA-DY-A1DF TCGA-F5-6571 TCGA-F5-6812 
       10.19        10.98        24.13        31.30         0.66 

$`10P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
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        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        34.65        36.53        14.53        32.91 
TCGA-A6-5657 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-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 
        0.99         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
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         0.99        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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        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        48.20        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 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        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-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        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         4.50        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-D5-6929 TCGA-D5-6930 
       12.43         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-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        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 
        1.28         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        43.07        61.87        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-G4-6320 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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        46.75        47.15        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       67.00        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         8.45        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         1.02         2.01 
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         4.60         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 
       60.03         7.99        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         7.10        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 
       14.86         0.39         1.02         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 
              0.66               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             91.79             140.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            15.950             18.015 
[1] "0.7 - 91.8 (15.9)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "1.9"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    35  11
  10P GAIN WILD-TYPE 403 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     35   11
  10P GAIN WILD-TYPE  403  151
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON                35                403
  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         4        0        1        15         1         0
  10P GAIN WILD-TYPE      98        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         73         45       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                   4                 98
  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                 73
  STAGE IIIC                8                 45
  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   3  38   4
  10P GAIN WILD-TYPE  19 102 374  61
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 19
  T2                3                102
  T3               38                374
  T4                4                 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
  10P GAIN MUTATED    21   9  16
  10P GAIN WILD-TYPE 320 139  96
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               21                320
  N1                9                139
  N2               16                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P GAIN MUTATED    31   6   2   0   5
  10P GAIN WILD-TYPE 415  68   8   2  58
D19V7, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                31                415
  M1                 6                 68
  M1A                2                  8
  M1B                0                  2
  MX                 5                 58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    22  24
  10P GAIN WILD-TYPE 261 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     22   24
  10P GAIN WILD-TYPE  261  297
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               22                261
  MALE                 24                297
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                     31                             4
  10P GAIN WILD-TYPE                  347                            55
                    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                         31                347
  COLON MUCINOUS ADENOCARCINOMA                 4                 55
  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  45
  10P GAIN WILD-TYPE   8 550
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   45
  10P GAIN WILD-TYPE    8  550
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 1                  8
  YES               45                550
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    34   1   3   2
  10P GAIN WILD-TYPE 402   4  33  27
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               34                402
  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                           5    26
  10P GAIN WILD-TYPE                        51   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                       5                 51
  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    19   5
  10Q GAIN WILD-TYPE 447 104
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                24                551 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                104 
$`10Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-4107 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3982 
        5.26        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         5.19         6.87         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-AF-2689 TCGA-AG-3999 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 
       36.00        17.95        28.04        70.03        10.19        10.98 

$`10Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        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 
       15.52        37.05        37.25        16.04        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-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-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 
        0.99         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
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         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.10         0.76         0.20         0.43         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-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        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        48.20        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 
        8.02        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        14.99        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         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        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         1.28 
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        43.07        61.87        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         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       67.00        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         8.45        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         1.02         2.01 
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-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        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-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-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        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         7.10 
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-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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.55               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             74.56             140.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            15.155             17.850 
[1] "1.6 - 74.6 (15.2)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    20   6
  10Q GAIN WILD-TYPE 418 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     20    6
  10Q GAIN WILD-TYPE  418  156
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON                20                418
  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         2        0        1         6         0         0
  10Q GAIN WILD-TYPE     100        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         74         48       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                   2                100
  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                 74
  STAGE IIIC                5                 48
  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   2  22   2
  10Q GAIN WILD-TYPE  20 103 390  63
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                 20
  T2                2                103
  T3               22                390
  T4                2                 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
  10Q GAIN MUTATED     9   8   9
  10Q GAIN WILD-TYPE 332 140 103
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                9                332
  N1                8                140
  N2                9                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  10Q GAIN MUTATED    16   3   1   0   4
  10Q GAIN WILD-TYPE 430  71   9   2  59
D20V7, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                16                430
  M1                 3                 71
  M1A                1                  9
  M1B                0                  2
  MX                 4                 59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    13  13
  10Q GAIN WILD-TYPE 270 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     13   13
  10Q GAIN WILD-TYPE  270  308
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               13                270
  MALE                 13                308
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                     16                             4
  10Q GAIN WILD-TYPE                  362                            55
                    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                         16                362
  COLON MUCINOUS ADENOCARCINOMA                 4                 55
  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  25
  10Q GAIN WILD-TYPE   8 570
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   25
  10Q GAIN WILD-TYPE    8  570
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                  8
  YES               25                570
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    20   0   1   2
  10Q GAIN WILD-TYPE 416   5  35  27
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               20                416
  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                           3    13
  10Q GAIN WILD-TYPE                        53   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                       3                 53
  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  15
  11P GAIN WILD-TYPE 402  94
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                79                496 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                 94 
$`11P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 
       37.02        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        52.44         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         1.02        16.31         0.95         6.87 
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        61.87        55.04 
TCGA-G4-6310 TCGA-G4-6314 TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-6655 
       45.11        35.93        30.28        17.23        10.39        20.02 
TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-4001 
       65.98        12.00        46.03        19.99        19.99        36.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 
        1.02        25.97        31.00         4.60        10.19         9.37 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
        4.73        11.01        12.99        12.00        36.00        30.05 
TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 
      126.44         2.40        16.31        13.64         0.39         1.02 
TCGA-G5-6233 
       18.28 

$`11P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        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-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-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-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 
        0.99         0.99        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-3848 
       17.98        15.95        38.99        36.95        14.93         0.99 
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-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
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         0.99        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-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.58         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20         0.43         0.46         0.92        14.50        27.09 
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         5.19         5.52 
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        48.20        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         8.02 
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        14.99        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         7.92        15.12         4.50        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 
        1.28         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        43.07        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       26.99        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       14.50         8.45        15.39        10.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95         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-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-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-A01W 
       15.95        36.03         9.07         1.02        12.00        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-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        0.72         1.81         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-6156 
       60.03         7.99        10.98        15.02        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
        7.10        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-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-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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       14.86         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 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            126.44             140.38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            19.990             17.375 
[1] "0.4 - 126.4 (20.0)" "0.1 - 140.4 (17.4)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    51  31
  11P GAIN WILD-TYPE 387 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     51   31
  11P GAIN WILD-TYPE  387  131
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON                51                387
  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      89        1       33       153         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0          5         13          9       12
  11P GAIN WILD-TYPE        26         16         65         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                 89
  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                 65
  STAGE IIIC                9                 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  58   4
  11P GAIN WILD-TYPE  16  88 354  61
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 16
  T2               17                 88
  T3               58                354
  T4                4                 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
  11P GAIN MUTATED    40  22  20
  11P GAIN WILD-TYPE 301 126  92
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               40                301
  N1               22                126
  N2               20                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  11P GAIN MUTATED    56  15   3   0   6
  11P GAIN WILD-TYPE 390  59   7   2  57
D21V7, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                56                390
  M1                15                 59
  M1A                3                  7
  M1B                0                  2
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    38  45
  11P GAIN WILD-TYPE 245 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     38   45
  11P GAIN WILD-TYPE  245  276
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               38                245
  MALE                 45                276
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                     50                             1
  11P GAIN WILD-TYPE                  328                            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                328
  COLON MUCINOUS ADENOCARCINOMA                 1                 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  80
  11P GAIN WILD-TYPE   6 515
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   80
  11P GAIN WILD-TYPE    6  515
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 3                  6
  YES               80                515
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    58   1   6   2
  11P GAIN WILD-TYPE 378   4  30  27
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               58                378
  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                           9    46
  11P GAIN WILD-TYPE                        47   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                       9                 47
  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    61  12
  11Q GAIN WILD-TYPE 405  97
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                73                502 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                 97 
$`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 
       52.44         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         0.99 
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         6.87        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-RU-A8FL 
       35.97        61.87        55.04        45.11        35.93        30.28 
TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3612 
       17.23        10.39        65.98        12.00        46.03        19.99 
TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 
        1.02        36.03         1.02        25.97        31.00         4.60 
TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        9.37         4.73        11.01        12.99        12.00        15.02 
TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 
       36.00       126.44        16.31        13.64         0.39         1.02 
TCGA-F5-6812 
        0.66 

$`11Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        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-A6-6137 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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        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-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       61.84         9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01         0.99        14.01        33.99        21.01        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-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        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-3854 
       17.98        15.95        38.99        36.95        14.93        36.03 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       32.05        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-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        17.03         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         0.99        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         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.10         0.76         0.20         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        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        48.20        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         8.02        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        14.99        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         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        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         1.28         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        43.07        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 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       14.76        67.00        24.13        17.95        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        37.74        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 
       20.02        10.39        86.63        11.84        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
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-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-3890 
       32.98         0.99         0.99        19.99        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-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-A015 
       13.94         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         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-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       38.04         0.49         1.45         0.69         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
       10.19         6.05         6.05         6.97        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.99        10.98        15.02        13.97         7.10        30.05 
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-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-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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       14.86         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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            126.44             140.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             20.98              17.72 
[1] "0.4 - 126.4 (21.0)" "0.1 - 140.4 (17.7)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    49  26
  11Q GAIN WILD-TYPE 389 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     49   26
  11Q GAIN WILD-TYPE  389  136
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON                49                389
  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      90        1       32       156         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          4         12          9        9
  11Q GAIN WILD-TYPE        26         17         66         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                 90
  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                 66
  STAGE IIIC                9                 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  52   5
  11Q GAIN WILD-TYPE  18  89 360  60
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 18
  T2               16                 89
  T3               52                360
  T4                5                 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
  11Q GAIN MUTATED    36  21  18
  11Q GAIN WILD-TYPE 305 127  94
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               36                305
  N1               21                127
  N2               18                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  11Q GAIN MUTATED    51  12   4   0   6
  11Q GAIN WILD-TYPE 395  62   6   2  57
D22V7, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                51                395
  M1                12                 62
  M1A                4                  6
  M1B                0                  2
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    35  40
  11Q GAIN WILD-TYPE 248 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     35   40
  11Q GAIN WILD-TYPE  248  281
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               35                248
  MALE                 40                281
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                     49                             0
  11Q GAIN WILD-TYPE                  329                            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                329
  COLON MUCINOUS ADENOCARCINOMA                 0                 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  73
  11Q GAIN WILD-TYPE   7 522
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2   73
  11Q GAIN WILD-TYPE    7  522
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 2                  7
  YES               73                522
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    54   1   4   2
  11Q GAIN WILD-TYPE 382   4  32  27
D22V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               54                382
  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                           9    39
  11Q GAIN WILD-TYPE                        47   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                       9                 47
  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  25
  12P GAIN WILD-TYPE 376  84
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               115                460 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                25                 84 
$`12P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
        5.06         5.26        44.91        13.94        16.04        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-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3560 
        1.02        58.03        29.00        29.00        12.99        19.99 
TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       78.08         0.92        11.01         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         0.99        35.05         0.99        37.02        14.93 
TCGA-AA-3851 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-A00K 
       33.07        12.99        24.00        26.01        24.00        18.05 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       12.00        31.00        51.98         0.92        22.03        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6963 TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK 
       40.96         0.07         0.10         0.92         0.20         6.87 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
        5.13        49.41         6.77         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4744 TCGA-CM-4747 
        3.06       102.44        40.34        15.62        20.02         8.02 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6678 
       16.01        15.02        21.99        13.02        14.04        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 
       20.19        17.75         4.50        14.30        11.64        13.41 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28M 
       12.00        10.26       119.70        24.43        44.32        95.18 
TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U 
        8.61        35.87        44.68        13.78        47.15        10.98 
TCGA-NH-A6GB TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 
        5.59        12.72        37.74         8.45        10.39        36.03 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3883 
       46.03         2.01         6.05        19.99         7.99         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G 
       36.95         1.02        36.03        15.95        36.03        38.96 
TCGA-AG-A02N TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       61.97        60.03        13.05        10.06         5.29       126.44 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 
       32.61        19.96        18.28        17.69        13.64        11.97 
TCGA-G5-6233 
       18.28 

$`12P GAIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        15.52        37.05        37.25 
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-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        23.61        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.69        24.39        19.66        20.28        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
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-3530 TCGA-AA-3531 TCGA-AA-3538 
       36.03         8.05        19.07        19.07        34.03        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 
       50.04        47.05        47.01        15.02        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       85.05        19.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       15.95        38.99        36.95        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-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-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
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         0.99        32.02 
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-A02W TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 
        2.01         5.03        41.00        18.05        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         1.58         1.02         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.43         0.46        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         5.19         5.52 
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-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 
      100.01        29.56         5.23        11.74         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         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        48.20        51.32        21.99        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-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.42        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       12.39        10.13        12.43         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 
       35.97        60.79       117.07        98.24        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18         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         1.28         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-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       43.07        61.87        53.62        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-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.04        35.80        26.17        91.79        46.75        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
        4.11        10.52         2.79         5.98         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       19.10        10.39        14.50        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 
        1.02         2.01        24.00         1.02        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       12.03         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-3890 
        1.02        32.98         0.99         0.99        19.99        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        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-A016 
       13.94         6.02        25.97        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        41.00        38.04         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         4.60         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-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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         7.10        30.05        12.95 
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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            126.44             140.38 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            16.010             17.965 
[1] "0.1 - 126.4 (16.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.3"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    94  33
  12P GAIN WILD-TYPE 344 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     94   33
  12P GAIN WILD-TYPE  344  129
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON                94                344
  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      83        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         69         41       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                 83
  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                 69
  STAGE IIIC               12                 41
  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  81 325  51
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                 19
  T2               24                 81
  T3               87                325
  T4               14                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P GAIN MUTATED    81  24  22
  12P GAIN WILD-TYPE 260 124  90
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               81                260
  N1               24                124
  N2               22                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  12P GAIN MUTATED    94  11   5   0  15
  12P GAIN WILD-TYPE 352  63   5   2  48
D23V7, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                94                352
  M1                11                 63
  M1A                5                  5
  M1B                0                  2
  MX                15                 48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    60  67
  12P GAIN WILD-TYPE 223 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     60   67
  12P GAIN WILD-TYPE  223  254
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               60                223
  MALE                 67                254
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                     80                            14
  12P GAIN WILD-TYPE                  298                            45
                    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                298
  COLON MUCINOUS ADENOCARCINOMA                14                 45
  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   6 471
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3  124
  12P GAIN WILD-TYPE    6  471
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 3                  6
  YES              124                471
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    94   1   5   6
  12P GAIN WILD-TYPE 342   4  31  23
D23V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               94                342
  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                        45   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                 45
  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    80  21
  12Q GAIN WILD-TYPE 386  88
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               101                474 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                 88 
$`12Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-4105 
        5.06         5.26        44.91        13.94        16.04        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-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3560 
        1.02        58.03        29.00        29.00        12.99        19.99 
TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       78.08         0.92         5.98        37.05         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 
        0.99        35.05         0.99        37.02        14.93        33.07 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-A00J 
       12.99        24.00        26.01        24.00        26.01        18.05 
TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R 
       18.05        12.00        31.00        51.98         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-6598 
       39.98        40.96         0.07         0.92         6.87        49.41 
TCGA-AZ-6599 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 
        6.77         1.94         2.24         3.06       102.44        40.34 
TCGA-CK-4952 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 
       15.62         8.02        16.01        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 
       14.04        11.01        20.19        17.75         4.50        14.30 
TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB 
       11.64        12.00        10.26       119.70        24.43        44.32 
TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 
       95.18        13.64        35.87        44.68        13.78        47.15 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3594 
       10.98         5.59        12.72         8.45        36.03         2.01 
TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A015 TCGA-AG-A02G 
       19.99         1.02         1.02        36.03        36.03        38.96 
TCGA-AG-A02N TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 
       61.97        13.05        10.06       126.44        32.61        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
       18.28        17.69        13.64        11.97        18.28 

$`12Q GAIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        15.52        37.05        37.25 
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-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        23.61        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.69        24.39        19.66        20.28        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
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-3530 TCGA-AA-3531 TCGA-AA-3538 
       36.03         8.05        19.07        19.07        34.03        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 
       50.04        47.05        47.01        15.02        11.01        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         0.99        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         0.99 
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-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01         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-3977 
       21.99        16.08        50.99        13.05        34.06        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-A00L TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K 
       34.98        15.02        15.02         0.99        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
        5.03        41.00        18.05        21.37         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         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.43         0.46        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         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19         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        48.20 
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-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32         7.92        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       12.43         9.04         9.44        13.41         1.51        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-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-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        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-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        46.75        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        65.98        11.84        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03        50.04        12.03         6.05         0.99        15.95 
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-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-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-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        41.00        38.04         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         4.60         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 
       60.03         7.99        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         7.10        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.95         5.29        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            126.44             140.38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            18.050             17.805 
[1] "0.1 - 126.4 (18.1)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    87  24
  12Q GAIN WILD-TYPE 351 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     87   24
  12Q GAIN WILD-TYPE  351  138
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON                87                351
  RECTUM               24                138
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q GAIN MUTATED        15        1        9        45         1         1
  12Q GAIN WILD-TYPE      87        0       27       126         9         2
                    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         69         45       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                  15                 87
  STAGE IA                  1                  0
  STAGE II                  9                 27
  STAGE IIA                45                126
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                6                 15
  STAGE IIIB                9                 69
  STAGE IIIC                8                 45
  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  21  76  12
  12Q GAIN WILD-TYPE  19  84 336  53
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                 19
  T2               21                 84
  T3               76                336
  T4               12                 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
  12Q GAIN MUTATED    74  25  12
  12Q GAIN WILD-TYPE 267 123 100
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               74                267
  N1               25                123
  N2               12                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  12Q GAIN MUTATED    87   7   5   0  11
  12Q GAIN WILD-TYPE 359  67   5   2  52
D24V7, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                87                359
  M1                 7                 67
  M1A                5                  5
  M1B                0                  2
  MX                11                 52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    55  56
  12Q GAIN WILD-TYPE 228 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     55   56
  12Q GAIN WILD-TYPE  228  265
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               55                228
  MALE                 56                265
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                     72                            15
  12Q GAIN WILD-TYPE                  306                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                      21                              2
  12Q GAIN WILD-TYPE                   125                             11
D24V9, multiclass
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         72                306
  COLON MUCINOUS ADENOCARCINOMA                15                 44
  RECTAL ADENOCARCINOMA                        21                125
  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   8 485
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1  110
  12Q GAIN WILD-TYPE    8  485
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  8
  YES              110                485
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    86   1   4   4
  12Q GAIN WILD-TYPE 350   4  32  25
D24V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               86                350
  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                          11    48
  12Q GAIN WILD-TYPE                        45   244
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                      11                 45
  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(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   281  66
  13Q GAIN WILD-TYPE 185  43
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               347                228 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                66                 43 
$`13Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
        5.06         5.26        37.02        46.65        43.76        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       24.69        23.87        20.28        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 
        1.02        37.05         1.02        58.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        9.07        24.03        36.03        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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        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-3679 
       78.08         6.05         2.01        14.01        50.04        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 
        5.98        37.05        19.00        85.05         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       35.05         0.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
        0.99        32.05         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3949 TCGA-AA-3955 
       27.02        29.98         2.01        12.99        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3982 
       34.03        16.08        50.99        13.05        26.01        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        42.02        14.99        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       12.00        31.00        33.04         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 
       41.00        39.98        40.96        21.37         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.20         0.43        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.95        15.75        21.44         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       50.37         1.41         5.13        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        2.24         3.06         0.07         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       48.20         2.01        20.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       22.03        22.98        30.08        16.01         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        15.02        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        12.26        19.59        13.51        11.51 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.50        17.13        12.49         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04        13.41        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
      119.70       130.65        92.75        49.91        13.32         7.50 
TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51         7.76         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.97        13.38         6.18        29.59        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       23.51        74.56        61.87        44.68        45.11        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        35.80        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        4.11        10.52         5.59         5.19         5.49        26.99 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 
       10.39        86.63        65.98        11.84         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 
        2.01         1.02        46.03        34.03         0.99        19.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3887 
       19.99         0.99        29.98         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        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-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        6.02        25.97        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04         0.49         0.69         0.72         4.60         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        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       10.98        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD 
        7.10        30.05        13.05        10.06        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-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-7002 TCGA-F5-6464 TCGA-F5-6465 
       16.41        11.51        10.78        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        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        55.76        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        23.38        17.79        37.05        37.25        16.04 
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        52.44         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-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        8.05        19.07        19.07        17.95        29.95        23.01 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       61.02         6.97        54.02         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 
       11.01        36.00         5.03        26.99        19.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 
        1.02        17.98        15.95        38.99        33.07        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       31.07        53.00        18.05        31.00        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3977 
       24.00         2.01         2.01        21.99        34.06        25.02 
TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       24.00        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
       27.02         0.99        17.03        21.99        34.98         0.99 
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-A02J TCGA-AA-A02O 
       26.01        37.02        39.06        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       22.03        18.05         0.07         4.21        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 
        0.76         0.46         0.92        27.09         0.20        17.82 
TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 
        5.52        58.39         5.65        32.94        83.80        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01         3.19         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.26         0.33         0.10        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-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 
       37.02         8.02        26.04        27.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       12.00        21.99        14.04        12.95        13.05        12.03 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       14.99        20.19        20.42        16.14        15.58        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 
        9.44        11.64         1.51        24.43        38.20        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G 
      140.38        44.32       135.65       139.17        81.37        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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 
       13.45        35.87         1.55        16.31         1.28        19.43 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       43.07        53.62        55.04        51.75        35.93        36.72 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U 
       22.09        26.04        13.78        26.17        52.80        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        2.79         5.98         1.32        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       67.00        12.72         8.45        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        8.02        24.00         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 
       15.95         7.99         1.02        32.98         0.99         1.02 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 
       13.02        48.03        20.98        13.94        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
        1.02        31.00        10.98        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6681 
        1.81        10.19         6.05        13.97        15.02        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 
        5.29       126.44         2.40        19.96        20.91         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       13.64        17.46         8.45         0.53         1.12         0.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            131.51             140.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             17.03              18.05 
[1] "0.1 - 131.5 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   248 110
  13Q GAIN WILD-TYPE 190  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    248  110
  13Q GAIN WILD-TYPE  190   52
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON               248                190
  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        59        0       18        86         4         3
  13Q GAIN WILD-TYPE      43        1       18        85         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED          15         17         52         36       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                  59                 43
  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               52                 26
  STAGE IIIC               36                 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  60 248  39
  13Q GAIN WILD-TYPE   6  45 164  26
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                  6
  T2               60                 45
  T3              248                164
  T4               39                 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   180 102  78
  13Q GAIN WILD-TYPE 161  46  34
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0              180                161
  N1              102                 46
  N2               78                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  13Q GAIN MUTATED   260  56   5   0  37
  13Q GAIN WILD-TYPE 186  18   5   2  26
D25V7, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               260                186
  M1                56                 18
  M1A                5                  5
  M1B                0                  2
  MX                37                 26
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   163 199
  13Q GAIN WILD-TYPE 120 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    163  199
  13Q GAIN WILD-TYPE  120  122
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE              163                120
  MALE                199                122
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                    232                            16
  13Q GAIN WILD-TYPE                  146                            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                        232                146
  COLON MUCINOUS ADENOCARCINOMA                16                 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     7 355
  13Q GAIN WILD-TYPE   2 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7  355
  13Q GAIN WILD-TYPE    2  240
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 7                  2
  YES              355                240
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   253   3  26  12
  13Q GAIN WILD-TYPE 183   2  10  17
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              253                183
  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                          33   189
  13Q GAIN WILD-TYPE                        23   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                      33                 23
  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    34   5
  14Q GAIN WILD-TYPE 432 104
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                536 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                104 
$`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        16.04        29.16        25.18        24.16 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3851 TCGA-AA-3941 
       26.01        12.99        20.98        78.08        33.07        24.00 
TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6890 TCGA-AD-6965 
        2.01        19.00         0.99         0.92         0.79         0.20 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6719 TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5539 
        3.19         2.24         1.35        15.02        11.01        19.59 
TCGA-D5-6538 TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6307 TCGA-G4-6626 
       17.13         6.12        95.18         1.55        55.04        46.75 
TCGA-G4-6627 TCGA-NH-A6GC TCGA-AF-6136 TCGA-AG-3999 TCGA-AG-A014 TCGA-AG-A01L 
       47.15         1.32        15.39        28.04        15.95        12.00 
TCGA-AG-A01Y TCGA-EI-6512 TCGA-EI-6885 
       64.01        17.69        13.64 

$`14Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        44.91        35.11        13.94        15.52 
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-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         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-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-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-3662 TCGA-AA-3663 
       19.99        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-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         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.99        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-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        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        17.03         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-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-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-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-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        1.58         1.02         0.10         0.76         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         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-5914 
       40.34        70.16        15.62        48.20        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         8.02        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-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        14.99        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-D5-6539 TCGA-D5-6540 
        7.92        15.12        17.85         4.50        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-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        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 
        1.28         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        43.07        61.87 
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-G4-6315 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         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.98         5.59         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        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         8.45        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         1.02         2.01        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         4.60         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 
       60.03         7.99        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         7.10        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        14.86         0.39         1.02         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 
              0.20               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             95.18             140.38 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             17.13              17.90 
[1] "0.2 - 95.2 (17.1)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    34   8
  14Q GAIN WILD-TYPE 404 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     34    8
  14Q GAIN WILD-TYPE  404  154
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON                34                404
  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      96        1       33       160        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          1          7          4        4
  14Q GAIN WILD-TYPE        26         20         71         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                 96
  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                 71
  STAGE IIIC                4                 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  30   5
  14Q GAIN WILD-TYPE  19  99 382  60
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                 19
  T2                6                 99
  T3               30                382
  T4                5                 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
  14Q GAIN MUTATED    22  11   9
  14Q GAIN WILD-TYPE 319 137 103
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               22                319
  N1               11                137
  N2                9                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  14Q GAIN MUTATED    28   4   3   1   6
  14Q GAIN WILD-TYPE 418  70   7   1  57
D26V7, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                28                418
  M1                 4                 70
  M1A                3                  7
  M1B                1                  1
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    19  23
  14Q GAIN WILD-TYPE 264 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     19   23
  14Q GAIN WILD-TYPE  264  298
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               19                264
  MALE                 23                298
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                     26                             8
  14Q GAIN WILD-TYPE                  352                            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                352
  COLON MUCINOUS ADENOCARCINOMA                 8                 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  41
  14Q GAIN WILD-TYPE   8 554
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   41
  14Q GAIN WILD-TYPE    8  554
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  8
  YES               41                554
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    29   0   1   3
  14Q GAIN WILD-TYPE 407   5  35  26
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               29                407
  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                           1    22
  14Q GAIN WILD-TYPE                        55   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                       1                 55
  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 455 106
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                561 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                106 
$`15Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-6649 TCGA-AA-3534 TCGA-AA-3941 TCGA-AZ-4614 TCGA-CA-5254 
        5.06        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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.26        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        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 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        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-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-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        17.03         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 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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         1.58         1.02         0.10         0.76         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        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 
       48.20        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         8.02        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        14.99        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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        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         1.28         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        43.07        61.87 
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         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        6.64        14.76        30.28        67.00        24.13        17.95 
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-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50         8.45        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         1.02         2.01        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-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-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         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        60.03         7.99        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         7.10 
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-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.24               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.39             140.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            16.385             17.850 
[1] "2.2 - 82.4 (16.4)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 427 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  427  158
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON                11                427
  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     100        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         77         52       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                100
  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                 77
  STAGE IIIC                1                 52
  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  20 103 404  60
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                 20
  T2                2                103
  T3                8                404
  T4                5                 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
  15Q GAIN MUTATED     8   3   4
  15Q GAIN WILD-TYPE 333 145 108
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                8                333
  N1                3                145
  N2                4                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  15Q GAIN MUTATED    11   3   1   0   0
  15Q GAIN WILD-TYPE 435  71   9   2  63
D27V7, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                11                435
  M1                 3                 71
  M1A                1                  9
  M1B                0                  2
  MX                 0                 63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 272 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  272  317
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                272
  MALE                  4                317
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                     10                             1
  15Q GAIN WILD-TYPE                  368                            58
                    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                368
  COLON MUCINOUS ADENOCARCINOMA                 1                 58
  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   8 581
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   14
  15Q GAIN WILD-TYPE    8  581
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 1                  8
  YES               14                581
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    11   0   1   1
  15Q GAIN WILD-TYPE 425   5  35  28
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               11                425
  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                        55   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                 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(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   115  20
  16P GAIN WILD-TYPE 351  89
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               135                440 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                 89 
$`16P GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       15.52        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         1.02         0.10         0.20         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 
       15.75         5.19         6.87         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 
       48.20        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 
       61.87        44.68        55.04        45.11        39.42        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-AF-2689 TCGA-AF-3911 
       13.78        46.75         5.59         1.32        17.95        37.74 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3726 TCGA-AG-3890 
       15.39        20.02        86.63        65.98         7.99        17.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       19.99        36.03         0.99        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 
       12.00        31.00        38.96        38.04         0.72        10.19 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
        6.97         9.37        60.03        11.01        12.99        12.00 
TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       10.06        24.13         0.49        17.69        16.31        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       14.86         0.39         0.76 

$`16P GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        16.04        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-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        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-3680 
       54.02         2.01        14.01         0.92        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 
        1.02        17.98        15.95        38.99         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        31.07        53.00        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 
        2.01        33.01        26.01        24.00         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       50.99        13.05        34.06        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
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-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-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-6899 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         1.58         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 
        0.46         0.92        14.50        27.09        16.31         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        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         8.02        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        14.99        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         7.92        17.85         4.50        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         1.28 
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        43.07        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        2.79         5.98         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
        6.64        14.76        30.28        67.00        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
        8.45        10.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        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-3727 TCGA-AG-3728 
        0.99        15.95        19.99        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-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-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       32.02        28.04        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00         0.49         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        1.81         6.05         6.05         4.73        13.97         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       10.98        15.02        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        31.30         1.02         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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.44             140.38 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            18.250             17.655 
[1] "0.1 - 102.4 (18.2)" "0.1 - 140.4 (17.7)"
[1] "hr=" "1.3"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   104  40
  16P GAIN WILD-TYPE 334 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    104   40
  16P GAIN WILD-TYPE  334  122
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON               104                334
  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        17        1        4        32         3         0
  16P GAIN WILD-TYPE      85        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         53         35       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                  17                 85
  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                 53
  STAGE IIIC               18                 35
  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  24  99  16
  16P GAIN WILD-TYPE  15  81 313  49
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 15
  T2               24                 81
  T3               99                313
  T4               16                 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
  16P GAIN MUTATED    63  46  35
  16P GAIN WILD-TYPE 278 102  77
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               63                278
  N1               46                102
  N2               35                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16P GAIN MUTATED    99  21   2   1  19
  16P GAIN WILD-TYPE 347  53   8   1  44
D28V7, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                99                347
  M1                21                 53
  M1A                2                  8
  M1B                1                  1
  MX                19                 44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    69  76
  16P GAIN WILD-TYPE 214 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     69   76
  16P GAIN WILD-TYPE  214  245
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               69                214
  MALE                 76                245
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                     98                             6
  16P GAIN WILD-TYPE                  280                            53
                    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                         98                280
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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     4 141
  16P GAIN WILD-TYPE   5 454
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  141
  16P GAIN WILD-TYPE    5  454
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                  5
  YES              141                454
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED   109   0  10   7
  16P GAIN WILD-TYPE 327   5  26  22
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0              109                327
  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                          14    69
  16P GAIN WILD-TYPE                        42   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                      14                 42
  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  21
  16Q GAIN WILD-TYPE 353  88
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               134                441 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                 88 
$`16Q GAIN MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6140 
       15.52        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         1.02         0.10 
TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 
        0.20         0.95        15.75         5.19         6.87         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        48.20        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         5.59 
TCGA-NH-A6GC TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 
        1.32        17.95        37.74        10.39        15.39        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 
       86.63        65.98        17.03        19.99        36.03         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G 
       15.95        36.03         9.07        12.00        31.00        38.96 
TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 
       38.04         0.72        10.19         9.37        60.03        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       12.99        12.00        10.06        24.13        51.48         0.49 
TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       17.69        16.31        37.51        14.86         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6863 
        0.69         0.76 

$`16Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        16.04        34.65        36.53        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-A6-6137 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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       29.00         0.99        14.01        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.99        36.03        32.05        31.07        31.07        53.00 
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-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       24.00         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       34.06        25.02        24.00        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        32.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-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-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.58         0.76         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.20        21.44        17.82 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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 
        8.02        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 
       14.99        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         7.92        17.85         4.50        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 
        1.28         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        43.07        61.87        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 
        4.11        10.98        10.52         2.79         5.98         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       67.00        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       12.72        14.50         8.45        10.39        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         1.02         2.01 
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-3892 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       14.01         1.02        48.03        32.02        28.04        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-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       23.01        37.02         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.97         1.94        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97         4.73        13.97         7.99        10.98        15.02 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
       31.30         1.02         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            102.44             140.38 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             17.74              17.85 
[1] "0.1 - 102.4 (17.7)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   101  41
  16Q GAIN WILD-TYPE 337 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    101   41
  16Q GAIN WILD-TYPE  337  121
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON               101                337
  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        16        1        4        31         2         0
  16Q GAIN WILD-TYPE      86        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         51         37       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                  16                 86
  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                 51
  STAGE IIIC               16                 37
  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  23  99  15
  16Q GAIN WILD-TYPE  15  82 313  50
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                5                 15
  T2               23                 82
  T3               99                313
  T4               15                 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
  16Q GAIN MUTATED    60  48  34
  16Q GAIN WILD-TYPE 281 100  78
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               60                281
  N1               48                100
  N2               34                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  16Q GAIN MUTATED    97  21   2   1  19
  16Q GAIN WILD-TYPE 349  53   8   1  44
D29V7, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                97                349
  M1                21                 53
  M1A                2                  8
  M1B                1                  1
  MX                19                 44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    68  75
  16Q GAIN WILD-TYPE 215 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     68   75
  16Q GAIN WILD-TYPE  215  246
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               68                215
  MALE                 75                246
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                     95                             6
  16Q GAIN WILD-TYPE                  283                            53
                    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                         95                283
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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     4 139
  16Q GAIN WILD-TYPE   5 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4  139
  16Q GAIN WILD-TYPE    5  456
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                  5
  YES              139                456
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED   109   0   9   6
  16Q GAIN WILD-TYPE 327   5  27  23
D29V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0              109                327
  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                          14    73
  16Q GAIN WILD-TYPE                        42   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                      14                 42
  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    34   2
  17P GAIN WILD-TYPE 432 107
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                539 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                107 
$`17P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-6142 
        5.06         5.26        16.04        36.53        29.19        25.08 
TCGA-A6-6652 TCGA-AA-3506 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3939 
       24.69        58.03        35.05         1.02        17.03        12.99 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-5344 
        2.01        13.05        34.06         0.07       102.44        22.03 
TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6929 TCGA-DM-A28M 
       14.04        11.01        15.12         4.50        13.41        95.18 
TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-AG-3587 TCGA-AG-3608 TCGA-AG-3609 
        1.55        74.56        36.00        46.03        15.95        19.99 
TCGA-AG-3882 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6623 TCGA-DC-6682 TCGA-G5-6641 
       19.99         1.02         4.60         9.37        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 
       37.02        46.65        43.76        43.43        23.38        17.79 
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        15.52 
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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04         0.99         0.99         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 
       15.95        38.99        36.95        37.02        14.93         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
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        17.03         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         0.99        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         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20         0.43         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         3.29         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        48.20        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         8.02 
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-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-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-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        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         7.92        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       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-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-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-F4-6805 
       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         1.28         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 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.72        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         4.11        10.98        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        5.98         5.59         1.32         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       17.29         6.64        14.76        30.28        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        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         8.45        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         1.02         2.01        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        60.03         7.99        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         7.10        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        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         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               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            102.44             140.38 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            15.995             17.950 
[1] "0.1 - 102.4 (16.0)" "0.1 - 140.4 (17.9)"
[1] "hr=" "3.6"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    27   9
  17P GAIN WILD-TYPE 411 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     27    9
  17P GAIN WILD-TYPE  411  153
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON                27                411
  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      93        1       36       161        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           0          2          4          5        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                 93
  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                4                 74
  STAGE IIIC                5                 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  23   3
  17P GAIN WILD-TYPE  17  98 389  62
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                3                 17
  T2                7                 98
  T3               23                389
  T4                3                 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  10   6
  17P GAIN WILD-TYPE 321 138 106
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               20                321
  N1               10                138
  N2                6                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  17P GAIN MUTATED    24   4   2   0   6
  17P GAIN WILD-TYPE 422  70   8   2  57
D30V7, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                24                422
  M1                 4                 70
  M1A                2                  8
  M1B                0                  2
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    17  19
  17P GAIN WILD-TYPE 266 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     17   19
  17P GAIN WILD-TYPE  266  302
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               17                266
  MALE                 19                302
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                     23                             4
  17P GAIN WILD-TYPE                  355                            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                         23                355
  COLON MUCINOUS ADENOCARCINOMA                 4                 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  36
  17P GAIN WILD-TYPE   9 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   36
  17P GAIN WILD-TYPE    9  559
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  9
  YES               36                559
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    26   0   2   2
  17P GAIN WILD-TYPE 410   5  34  27
D30V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               26                410
  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                           4    17
  17P GAIN WILD-TYPE                        52   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                       4                 52
  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    92  13
  17Q GAIN WILD-TYPE 374  96
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               105                470 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                 96 
$`17Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 TCGA-A6-3810 
        5.06         5.26        43.43        17.79        16.04        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-AA-A02W 
       34.06        17.03        21.99        12.00         1.02        41.00 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-5407 
        4.21         0.79         0.10         0.43        16.31        61.41 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5341 
       29.56         3.19         0.07       102.44         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 
       13.05        11.08        11.01        19.59        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A1D0 
        1.32        15.12         4.50        17.13        13.41       130.65 
TCGA-DM-A285 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        6.12        95.18        74.56        61.87        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-RU-A8FL TCGA-AF-2690 
       39.42        36.00        26.43        46.75        30.28        17.23 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 
       86.63        11.84        12.00        46.03        34.03        15.95 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       19.99        19.99        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 
        9.07        31.00         0.69         4.60         6.05        12.00 
TCGA-DC-6682 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       13.05        51.48        17.00        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6641 
        1.02         0.46        26.43 

$`17Q GAIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        15.52        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        21.76        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
        9.63         5.03         1.02         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        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-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-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04         0.99         0.99         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 
       15.95        38.99        36.95        37.02        14.93         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       21.99        16.08        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-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-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       21.37        56.55         0.72         1.58         1.02         0.76 
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         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        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-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-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-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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        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-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
        8.02        26.04        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       16.01        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       12.00        16.04        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        11.08        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       12.26        13.51        20.19        20.42        17.75         7.92 
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-D5-6924 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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        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         1.28         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        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6321 
       53.62        44.68        51.75        35.93        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.04        13.78        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         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
        6.64        14.76        67.00        24.13        17.95        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-A56L TCGA-AG-3574 
        8.45        15.39        20.02        10.39        65.98        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         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
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-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         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-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02        36.03         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         1.81        10.19         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        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        19.96        20.91        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            130.65             140.38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             17.13              17.95 
[1] "0.1 - 130.7 (17.1)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.6"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    80  30
  17Q GAIN WILD-TYPE 358 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     80   30
  17Q GAIN WILD-TYPE  358  132
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON                80                358
  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        17        0        3        29         0         0
  17Q GAIN WILD-TYPE      85        1       33       142        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           4          5         14         11       15
  17Q GAIN WILD-TYPE        22         16         64         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                  17                 85
  STAGE IA                  0                  1
  STAGE II                  3                 33
  STAGE IIA                29                142
  STAGE IIB                 0                 10
  STAGE IIC                 0                  3
  STAGE III                 4                 22
  STAGE IIIA                5                 16
  STAGE IIIB               14                 64
  STAGE IIIC               11                 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  20  76   9
  17Q GAIN WILD-TYPE  15  85 336  56
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                 15
  T2               20                 85
  T3               76                336
  T4                9                 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
  17Q GAIN MUTATED    57  30  22
  17Q GAIN WILD-TYPE 284 118  90
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               57                284
  N1               30                118
  N2               22                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  17Q GAIN MUTATED    71  18   4   1  16
  17Q GAIN WILD-TYPE 375  56   6   1  47
D31V7, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                71                375
  M1                18                 56
  M1A                4                  6
  M1B                1                  1
  MX                16                 47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    51  59
  17Q GAIN WILD-TYPE 232 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51   59
  17Q GAIN WILD-TYPE  232  262
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               51                232
  MALE                 59                262
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                     72                             7
  17Q GAIN WILD-TYPE                  306                            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                         72                306
  COLON MUCINOUS ADENOCARCINOMA                 7                 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     1 109
  17Q GAIN WILD-TYPE   8 486
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1  109
  17Q GAIN WILD-TYPE    8  486
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 1                  8
  YES              109                486
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    78   1  10   2
  17Q GAIN WILD-TYPE 358   4  26  27
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               78                358
  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                          11    60
  17Q GAIN WILD-TYPE                        45   232
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                      11                 45
  WHITE                                          60                232
[1] 4 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    24   7
  18P GAIN WILD-TYPE 442 102
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                31                544 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                102 
$`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         0.99         0.99 
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        10.52         5.98 
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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6654 TCGA-A6-6780 
       25.18        20.61        21.76        24.69        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04         0.99 
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-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        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-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        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         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         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-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        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        48.20        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 
        8.02        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 
       14.99        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         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.50        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         1.28         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        43.07        61.87 
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         4.11        10.98         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        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 
        8.45        15.39        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07         1.02         2.01 
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-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-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-A02N TCGA-AG-A02X 
       10.98        51.98        49.97         1.94        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         4.60 
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        60.03         7.99        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 
        7.10        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-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        37.51        31.30        14.86         0.39         1.02 
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 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.24             140.38 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             11.08              18.05 
[1] "0.1 - 98.2 (11.1)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    25   8
  18P GAIN WILD-TYPE 413 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     25    8
  18P GAIN WILD-TYPE  413  154
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON                25                413
  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      97        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         75         46       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                 97
  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                 75
  STAGE IIIC                7                 46
  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  99 390  60
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                 20
  T2                6                 99
  T3               22                390
  T4                5                 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
  18P GAIN MUTATED    14   6  13
  18P GAIN WILD-TYPE 327 142  99
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               14                327
  N1                6                142
  N2               13                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  18P GAIN MUTATED    24   3   0   1   4
  18P GAIN WILD-TYPE 422  71  10   1  59
D32V7, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                24                422
  M1                 3                 71
  M1A                0                 10
  M1B                1                  1
  MX                 4                 59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    11  22
  18P GAIN WILD-TYPE 272 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11   22
  18P GAIN WILD-TYPE  272  299
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                272
  MALE                 22                299
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                     18                             7
  18P GAIN WILD-TYPE                  360                            52
                    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                360
  COLON MUCINOUS ADENOCARCINOMA                 7                 52
  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   8 563
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   32
  18P GAIN WILD-TYPE    8  563
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  8
  YES               32                563
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    23   0   1   1
  18P GAIN WILD-TYPE 413   5  35  28
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               23                413
  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                        53   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                 53
  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    15   3
  18Q GAIN WILD-TYPE 451 106
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                557 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                106 
$`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         0.99         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-AG-3600 TCGA-DT-5265 TCGA-F5-6464 
       98.24        74.56        10.39         6.05         5.29         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.18        24.16        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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        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-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         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 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        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 
        1.58         1.02         0.10         0.76         0.20         0.43 
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-A8YK 
       15.75        21.44        17.82         5.19         5.52         6.87 
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        48.20 
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         8.02        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 
       14.99        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         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.50        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         1.28         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 
       43.07        61.87        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        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         8.45        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        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-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 
        4.60         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        60.03         7.99        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         7.10        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-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.24             140.38 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.26              18.05 
[1] "0.1 - 98.2 (10.3)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    15   5
  18Q GAIN WILD-TYPE 423 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     15    5
  18Q GAIN WILD-TYPE  423  157
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON                15                423
  RECTUM                5                157
[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      98        1       33       168        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           3          1          0          4        2
  18Q GAIN WILD-TYPE        23         20         78         49       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                 98
  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                 78
  STAGE IIIC                4                 49
  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  12   4
  18Q GAIN WILD-TYPE  20 101 400  61
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                 20
  T2                4                101
  T3               12                400
  T4                4                 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
  18Q GAIN MUTATED    10   3   7
  18Q GAIN WILD-TYPE 331 145 105
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               10                331
  N1                3                145
  N2                7                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  18Q GAIN MUTATED    15   1   0   0   3
  18Q GAIN WILD-TYPE 431  73  10   2  60
D33V7, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                15                431
  M1                 1                 73
  M1A                0                 10
  M1B                0                  2
  MX                 3                 60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  14
  18Q GAIN WILD-TYPE 277 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   14
  18Q GAIN WILD-TYPE  277  307
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                277
  MALE                 14                307
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                     10                             5
  18Q GAIN WILD-TYPE                  368                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                       4                              1
  18Q GAIN WILD-TYPE                   142                             12
D33V9, multiclass
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                368
  COLON MUCINOUS ADENOCARCINOMA                 5                 54
  RECTAL ADENOCARCINOMA                         4                142
  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  19
  18Q GAIN WILD-TYPE   8 576
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   19
  18Q GAIN WILD-TYPE    8  576
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                  8
  YES               19                576
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    14   0   0   1
  18Q GAIN WILD-TYPE 422   5  36  28
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               14                422
  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                        56   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                 56
  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    79  16
  19P GAIN WILD-TYPE 387  93
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                95                480 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                 93 
$`19P GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
        5.06         5.26        37.02        43.43        45.60        15.52 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       16.04        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        52.44        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         1.58         1.02 
TCGA-AD-A5EK TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 
        0.43         6.87        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         8.02        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         5.19 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 
       17.95        17.23        86.63        65.98         1.02        46.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 
        6.05        19.99         0.99        19.99         1.02        36.03 
TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 
        1.02        15.95        12.00        31.00         1.94        38.04 
TCGA-CI-6619 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 
        6.05        10.98        11.01        12.00        36.00        13.05 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6863 
      129.27        20.55        17.69        16.31         0.76 

$`19P GAIN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        23.38        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       35.11        13.94        37.05        37.25        34.65        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-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 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         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        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         0.99 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 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-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-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        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-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         0.10         0.76         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-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         5.52        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        48.20        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        14.99        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 
        7.92        17.85         4.50        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         1.28 
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        43.07        61.87        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 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        67.00        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         8.45        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         2.01        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         4.60         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 
       60.03         7.99        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 
        7.10        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 
       14.86         0.39         1.02         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 
              0.43               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             140.38 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            17.690             17.835 
[1] "0.4 - 129.3 (17.7)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    70  32
  19P GAIN WILD-TYPE 368 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     70   32
  19P GAIN WILD-TYPE  368  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON                70                368
  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        16        0        5        31         0         0
  19P GAIN WILD-TYPE      86        1       31       140        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           4          3         18          6       12
  19P GAIN WILD-TYPE        22         18         60         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                  16                 86
  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                 60
  STAGE IIIC                6                 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  17  73  10
  19P GAIN WILD-TYPE  18  88 339  55
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                2                 18
  T2               17                 88
  T3               73                339
  T4               10                 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
  19P GAIN MUTATED    56  31  15
  19P GAIN WILD-TYPE 285 117  97
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               56                285
  N1               31                117
  N2               15                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  19P GAIN MUTATED    70  14   3   0  15
  19P GAIN WILD-TYPE 376  60   7   2  48
D34V7, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                70                376
  M1                14                 60
  M1A                3                  7
  M1B                0                  2
  MX                15                 48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    42  60
  19P GAIN WILD-TYPE 241 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     42   60
  19P GAIN WILD-TYPE  241  261
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               42                241
  MALE                 60                261
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                     64                             6
  19P GAIN WILD-TYPE                  314                            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                         64                314
  COLON MUCINOUS ADENOCARCINOMA                 6                 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     1 101
  19P GAIN WILD-TYPE   8 494
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1  101
  19P GAIN WILD-TYPE    8  494
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                  8
  YES              101                494
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    74   2   5   7
  19P GAIN WILD-TYPE 362   3  31  22
D34V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               74                362
  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                          13    55
  19P GAIN WILD-TYPE                        43   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                      13                 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(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    87  16
  19Q GAIN WILD-TYPE 379  93
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               103                472 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 93 
$`19Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
        5.06         5.26        37.02        43.43        45.60        15.52 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 
       16.04        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        52.44        35.01 
TCGA-AA-3506 TCGA-AA-3542 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3854 TCGA-AA-3939 
       58.03        12.99        35.05         0.99        36.03        12.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01G 
       50.99        13.05        18.05        27.02        42.02        12.00 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-6196 
       51.98         0.92         1.58         1.02         0.43         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 
        5.52         6.87        61.41        29.56        11.74         3.06 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 
        1.35        40.34        21.99         2.01        37.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       13.02        29.06        16.01         5.03        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        21.99        11.08        19.59        15.12 
TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F 
        4.50        11.64        12.00        11.38       119.70        35.97 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6311 
        8.61        13.64        35.41        82.39        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-AF-2689 TCGA-AF-A56K TCGA-AF-A56L 
       26.43        47.15         5.19        17.95        86.63        65.98 
TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 
       46.03        19.99         0.99        19.99         1.02         1.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 
       15.95        36.03         9.07        12.00        31.00         1.94 
TCGA-AG-A032 TCGA-CI-6619 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 
       38.04         6.05        13.97        11.01        12.00        36.00 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 
       13.05       129.27        20.55        17.69        16.31        13.64 
TCGA-F5-6863 
        0.76 

$`19Q GAIN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        23.38        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       35.11        13.94        37.05        37.25        34.65        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-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
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-A6-6782 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         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05         1.02        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-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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04         0.99         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-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        17.03         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         2.01         5.03        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
       15.75        21.44        17.82         5.19        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        48.20        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 
       21.14         2.93       124.27        23.05        20.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
        8.02        27.02        22.03        22.98        30.08        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        17.03        12.00        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        14.99        12.26 
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-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32         7.92        17.85        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-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD 
        9.04         9.44        13.41         1.51        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        13.38        11.11 
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-F4-6856 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        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        43.07        61.87 
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-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       17.29         6.64        14.76        30.28        67.00        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        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         8.45        15.39        20.02        10.39 
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-3593 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       50.04        12.03         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-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-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-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       23.01        37.02         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.97        38.96        61.97        41.00         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         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37         4.73        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       10.98        15.02        12.99        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         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 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             140.38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             16.31              17.90 
[1] "0.2 - 129.3 (16.3)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    79  32
  19Q GAIN WILD-TYPE 359 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     79   32
  19Q GAIN WILD-TYPE  359  130
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON                79                359
  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        20        0        4        32         0         0
  19Q GAIN WILD-TYPE      82        1       32       139        10         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           3          4         18          8       14
  19Q GAIN WILD-TYPE        23         17         60         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                  20                 82
  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                 60
  STAGE IIIC                8                 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  20  76  12
  19Q GAIN WILD-TYPE  17  85 336  53
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 17
  T2               20                 85
  T3               76                336
  T4               12                 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
  19Q GAIN MUTATED    60  34  17
  19Q GAIN WILD-TYPE 281 114  95
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               60                281
  N1               34                114
  N2               17                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  19Q GAIN MUTATED    74  16   4   0  16
  19Q GAIN WILD-TYPE 372  58   6   2  47
D35V7, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                74                372
  M1                16                 58
  M1A                4                  6
  M1B                0                  2
  MX                16                 47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48  63
  19Q GAIN WILD-TYPE 235 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48   63
  19Q GAIN WILD-TYPE  235  258
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               48                235
  MALE                 63                258
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                     69                            10
  19Q GAIN WILD-TYPE                  309                            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                         69                309
  COLON MUCINOUS ADENOCARCINOMA                10                 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     1 110
  19Q GAIN WILD-TYPE   8 485
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1  110
  19Q GAIN WILD-TYPE    8  485
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  8
  YES              110                485
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    79   2   6   7
  19Q GAIN WILD-TYPE 357   3  30  22
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               79                357
  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                          15    59
  19Q GAIN WILD-TYPE                        41   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                      15                 41
  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   266  65
  20P GAIN WILD-TYPE 200  44
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               331                244 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                 44 
$`20P GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
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-A6-5662 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       29.19        23.61        27.09        25.08        25.18        24.16 
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-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        6.97         1.02        36.03        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 
       29.00        12.99        14.01        21.01        13.02        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        19.99         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       50.04        47.05        15.02        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05         0.99        35.05         0.99        25.02 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        31.07        17.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       12.99        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U 
        7.96        13.94        18.05        17.03         4.01        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E 
       31.00        31.00        33.04        26.01        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 
        2.01         5.03         0.92        41.00        39.98         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.10         0.43         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 
       15.75         5.19         5.52         6.87         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       83.80        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       48.20        20.02         8.02         8.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        14.99        12.26 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6539 
       19.59        20.19        17.75         1.32        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        7.53        12.39        10.13         9.04        11.64        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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       13.32        12.59         7.50       139.17         6.12        14.04 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6855 
       13.45         6.18         1.55        29.59        33.67        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
      107.67        28.21        82.39        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.72        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       47.15         4.11         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 
       17.29        24.13        17.95        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         8.45        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         1.02         2.01        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-3902 
       36.95        17.03        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-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-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       51.98        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-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        9.37         4.73        13.97        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         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
       30.05        12.95       126.44        41.36       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69        16.31        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97         9.96        37.51         0.39         1.02         0.66 
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 
TCGA-G5-6641 
       26.43 

$`20P GAIN WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        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        52.44         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         0.99         1.02        17.98        15.95        36.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 
       36.03        32.05        53.00        24.03        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 
        2.01        33.01        26.01        24.00         2.01         2.01 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       34.06        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       15.02        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J 
       37.02        39.06        39.98        22.03        18.05        40.96 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
       56.55         0.76         0.20         0.92        27.09         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       21.44        17.82        75.25        50.37        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       32.94        22.36        61.41         6.77       100.01        11.74 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
        3.25         0.26         0.33         0.10        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-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 
       23.05        37.02        26.04        27.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6170 
       16.01        15.02        12.00        29.03        12.99        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       12.95        13.05        10.06        12.03        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.42        18.25         7.92        15.12         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       16.14        15.58        12.43        14.30         9.44         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       12.00        92.75        49.91       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      135.65         7.76        26.47        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
       11.11        13.64        35.87        16.31        16.24         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43         8.35        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 
       61.87        53.62        44.68        51.75        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       22.09        35.80        26.17        52.80        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        2.79         5.98         5.19         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 
       67.00        43.04        13.55        12.72        14.50        15.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 
       86.63        11.84        36.03        12.00        32.02         2.01 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3892 
        6.05         0.99         7.99        32.98        19.99        13.02 
TCGA-AG-3893 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J 
       35.01         0.99        20.98        13.94        15.95         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       12.00        31.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 
        1.94        38.96        61.97         6.05        60.03         7.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 
       13.05        10.06         5.29        57.24        51.48         0.49 
TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       19.96        16.34        16.41         8.61        17.46         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       31.30        14.86         0.69         0.46 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            139.17             140.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            16.310             20.515 
[1] "0.1 - 139.2 (16.3)" "0.1 - 140.4 (20.5)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   237 108
  20P GAIN WILD-TYPE 201  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    237  108
  20P GAIN WILD-TYPE  201   54
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON               237                201
  RECTUM              108                 54
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P GAIN MUTATED        61        1       13        87         4         2
  20P GAIN WILD-TYPE      41        0       23        84         6         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          13         19         40         31       47
  20P GAIN WILD-TYPE        13          2         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                  61                 41
  STAGE IA                  1                  0
  STAGE II                 13                 23
  STAGE IIA                87                 84
  STAGE IIB                 4                  6
  STAGE IIC                 2                  1
  STAGE III                13                 13
  STAGE IIIA               19                  2
  STAGE IIIB               40                 38
  STAGE IIIC               31                 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    13  65 233  34
  20P GAIN WILD-TYPE   7  40 179  31
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               13                  7
  T2               65                 40
  T3              233                179
  T4               34                 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  72
  20P GAIN WILD-TYPE 160  57  40
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              181                160
  N1               91                 57
  N2               72                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20P GAIN MUTATED   245  54   9   1  33
  20P GAIN WILD-TYPE 201  20   1   1  30
D36V7, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               245                201
  M1                54                 20
  M1A                9                  1
  M1B                1                  1
  MX                33                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   153 194
  20P GAIN WILD-TYPE 130 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    153  194
  20P GAIN WILD-TYPE  130  127
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              153                130
  MALE                194                127
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                    217                            19
  20P GAIN WILD-TYPE                  161                            40
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                     101                              5
  20P GAIN WILD-TYPE                    45                              8
D36V9, multiclass
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        217                161
  COLON MUCINOUS ADENOCARCINOMA                19                 40
  RECTAL ADENOCARCINOMA                       101                 45
  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"
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 340
  20P GAIN WILD-TYPE   2 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  340
  20P GAIN WILD-TYPE    2  255
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                  2
  YES              340                255
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   246   3  25  11
  20P GAIN WILD-TYPE 190   2  11  18
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              246                190
  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                          29   173
  20P GAIN WILD-TYPE                        27   119
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                      29                 27
  WHITE                                         173                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   353  81
  20Q GAIN WILD-TYPE 113  28
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               434                141 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                81                 28 
$`20Q GAIN MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
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-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
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-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       35.05         0.99        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        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-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        19.07         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        17.03         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       12.00        31.00        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        4.21         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.20         0.43         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       15.75         0.20         5.19         5.52         6.87        75.25 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13        83.80        22.36        65.00        62.79 
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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        2.01        20.02        37.02         8.02         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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       11.01        11.08        11.08        11.01        10.06        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       12.26        19.59        13.51        11.51        20.19        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         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        11.64        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        7.50        44.32       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       47.15         4.11         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       26.99        17.29         6.64        30.28        24.13        17.95 
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 
        8.45        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         1.02         2.01 
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         4.60         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         7.99        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         7.10        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        14.86         0.39         1.02         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 
        5.26        46.65        23.38        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         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 
       17.98        15.95        36.03        53.00        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R 
       38.07         1.02        35.01        35.01        39.06        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       18.05        56.55         0.76         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 
       17.82        50.37        58.39         5.65        32.94        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
        6.77       100.01        11.74         3.25         0.33         0.10 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6168 
       23.05        26.04        27.02        15.02        12.00        12.99 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6540 
       12.95        13.05        12.03        20.42         7.92        16.14 
TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D9 
       15.58         9.44         1.51        12.00        92.75       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      131.51       135.65         7.76        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       11.11        35.87        19.43        43.07        53.62        51.75 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       22.09        35.80        26.17        52.80        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 
        2.79         5.98        14.76        67.00        13.55        12.72 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 
       12.00        32.02         2.01         6.05        32.98        13.02 
TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CL-5917 TCGA-DT-5265 TCGA-EI-6507 
       20.98        49.97        61.97        60.03         5.29        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        8.61        17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            139.17             140.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             17.03              21.14 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.1)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   308 144
  20Q GAIN WILD-TYPE 130  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    308  144
  20Q GAIN WILD-TYPE  130   18
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON               308                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        77        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         61         43       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                  77                 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               61                 17
  STAGE IIIC               43                 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  84 311  44
  20Q GAIN WILD-TYPE   6  21 101  21
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               14                  6
  T2               84                 21
  T3              311                101
  T4               44                 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   237 126  89
  20Q GAIN WILD-TYPE 104  22  23
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              237                104
  N1              126                 22
  N2               89                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20Q GAIN MUTATED   325  67   9   1  47
  20Q GAIN WILD-TYPE 121   7   1   1  16
D37V7, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               325                121
  M1                67                  7
  M1A                9                  1
  M1B                1                  1
  MX                47                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   207 248
  20Q GAIN WILD-TYPE  76  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    207  248
  20Q GAIN WILD-TYPE   76   73
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              207                 76
  MALE                248                 73
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                    283                            24
  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                        283                 95
  COLON MUCINOUS ADENOCARCINOMA                24                 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     8 447
  20Q GAIN WILD-TYPE   1 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  447
  20Q GAIN WILD-TYPE    1  148
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                  1
  YES              447                148
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   327   4  32  16
  20Q GAIN WILD-TYPE 109   1   4  13
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              327                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                          38   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                      38                 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    22   6
  21Q GAIN WILD-TYPE 444 103
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                28                547 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                103 
$`21Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-5662 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
        5.26        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-RU-A8FL TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-A011 
       82.39        10.52        30.28        19.99        32.98        37.02 
TCGA-AH-6644 TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
        0.72         9.37         0.49        13.64 

$`21Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        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 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        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-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-3679 
        6.97        54.02        14.01         0.92        47.05        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         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
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        17.03 
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         0.99        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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09        16.31        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82         5.19         5.52         6.87        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        48.20        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 
        8.02        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        14.99        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 
        7.92        15.12        17.85         4.50        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         1.28         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        43.07        61.87        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         4.11        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       26.99        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        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         8.45        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         1.02         2.01        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         4.60         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        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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         7.10        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 
       14.86         0.39         1.02         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               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             95.18             140.38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            15.535             17.850 
[1] "0.5 - 95.2 (15.5)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21  10
  21Q GAIN WILD-TYPE 417 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21   10
  21Q GAIN WILD-TYPE  417  152
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON                21                417
  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         7        0        1         6         1         0
  21Q GAIN WILD-TYPE      95        1       35       165         9         3
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           2          2          5          1        4
  21Q GAIN WILD-TYPE        24         19         73         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                   7                 95
  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                 73
  STAGE IIIC                1                 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   6  21   2
  21Q GAIN WILD-TYPE  17  99 391  63
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 17
  T2                6                 99
  T3               21                391
  T4                2                 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
  21Q GAIN MUTATED    15   9   7
  21Q GAIN WILD-TYPE 326 139 105
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               15                326
  N1                9                139
  N2                7                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  21Q GAIN MUTATED    21   5   1   0   4
  21Q GAIN WILD-TYPE 425  69   9   2  59
D38V7, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                21                425
  M1                 5                 69
  M1A                1                  9
  M1B                0                  2
  MX                 4                 59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16  16
  21Q GAIN WILD-TYPE 267 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16   16
  21Q GAIN WILD-TYPE  267  305
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               16                267
  MALE                 16                305
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                     17                             4
  21Q GAIN WILD-TYPE                  361                            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                         17                361
  COLON MUCINOUS ADENOCARCINOMA                 4                 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  32
  21Q GAIN WILD-TYPE   9 563
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   32
  21Q GAIN WILD-TYPE    9  563
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  9
  YES               32                563
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    20   0   1   2
  21Q GAIN WILD-TYPE 416   5  35  27
D38V11, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               20                416
  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                           3    18
  21Q GAIN WILD-TYPE                        53   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                       3                 53
  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 448 104
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                552 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                104 
$`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         0.99         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         1.02        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         4.60         9.37        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6141 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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-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-3811 
       36.00         5.03        85.05        26.99        19.04         0.99 
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-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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 
       17.03         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         0.99 
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-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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        48.20        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         8.02        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        14.99        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         7.92        15.12        17.85         4.50        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         1.28 
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        43.07        61.87        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         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        10.52         2.79         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       67.00        24.13        17.95        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         8.45        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-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        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-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95         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-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        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-A011 
        0.99        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         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        60.03         7.99        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         7.10        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-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        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         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 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.99               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            102.44             140.38 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             19.99              17.77 
[1] "1.0 - 102.4 (20.0)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 425 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   10
  22Q GAIN WILD-TYPE  425  152
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON                13                425
  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      97        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         74         49       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                 97
  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                 74
  STAGE IIIC                4                 49
  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  18 102 394  65
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                2                 18
  T2                3                102
  T3               18                394
  T4                0                 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
  22Q GAIN MUTATED    10   6   7
  22Q GAIN WILD-TYPE 331 142 105
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               10                331
  N1                6                142
  N2                7                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  22Q GAIN MUTATED    17   5   0   0   1
  22Q GAIN WILD-TYPE 429  69  10   2  62
D39V7, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                17                429
  M1                 5                 69
  M1A                0                 10
  M1B                0                  2
  MX                 1                 62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10  13
  22Q GAIN WILD-TYPE 273 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10   13
  22Q GAIN WILD-TYPE  273  308
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               10                273
  MALE                 13                308
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                     13                             0
  22Q GAIN WILD-TYPE                  365                            59
                    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                365
  COLON MUCINOUS ADENOCARCINOMA                 0                 59
  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   8 573
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   22
  22Q GAIN WILD-TYPE    8  573
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                  8
  YES               22                573
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    16   0   3   0
  22Q GAIN WILD-TYPE 420   5  33  29
D39V11, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               16                420
  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                        55   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                 55
  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 = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    77  20
  XQ GAIN WILD-TYPE 389  89
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               97               478 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20                89 
$`XQ GAIN MUTATED`
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-6142 TCGA-A6-6650 
        5.26        44.91        45.60        16.04        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        52.44        36.03        29.00        24.00 
TCGA-AA-3558 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 
       20.98        54.02        14.01        47.01         5.98         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3844 TCGA-AA-3869 TCGA-AA-3994 
        0.99        35.05         0.99        14.93        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y 
       13.94        31.00        33.04        51.98         0.92        39.98 
TCGA-AD-6888 TCGA-AD-A5EK TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4614 
        4.21         0.43         0.20         5.19         6.87         5.65 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6719 TCGA-CK-5914 
       22.36        49.41       100.01         1.94         1.35        21.99 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 
       22.98        16.01         5.03        15.02        21.99        14.99 
TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       13.05        19.59        15.12         4.50        17.13        12.49 
TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28K 
       12.43       119.70         7.50         6.12        35.97        98.24 
TCGA-DM-A28M TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       95.18         6.18        74.56        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-NH-A6GB TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 
       39.42         5.59        67.00        13.55        10.39         8.45 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 TCGA-AG-3999 
       20.02        86.63        19.99        19.99        35.01        28.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A032 
        1.02         0.99        15.95        36.03         9.07        38.04 
TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 
        0.72         9.37        60.03        10.98        12.00        15.02 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       18.28        17.69        13.64         9.96        37.51         0.39 
TCGA-F5-6863 
        0.76 

$`XQ GAIN WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        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-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.18        24.16        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.05         6.97         2.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.05        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3821 
       85.05        26.99        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-3846 
       17.98        15.95        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         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         0.99        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        5.52        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        83.80        65.00        62.79        61.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19         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-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-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        48.20        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         8.02        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-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        15.02        17.03        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       29.03        16.04        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-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        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         7.92        17.85 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         7.53        12.39        10.13        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-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      119.93        60.79       117.07         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45        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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       61.87        53.62        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-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        47.15        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-2687 
       26.99        17.29         6.64        14.76        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        43.04        19.10        12.72        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       14.50        15.39        10.39        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         1.02         2.01 
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-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-3894 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        36.03        14.04        17.03 
TCGA-AG-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-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69         4.60         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         7.99 
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         7.10 
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-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-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-F5-6571 TCGA-F5-6702 
       10.78        17.46        11.97         8.45        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         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 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.20              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           119.70            140.38 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           17.690            17.835 
[1] "0.2 - 119.7 (17.7)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    73  30
  XQ GAIN WILD-TYPE 365 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     73   30
  XQ GAIN WILD-TYPE  365  132
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON               73               365
  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        14        0        8        24         1         0
  XQ GAIN WILD-TYPE      88        1       28       147         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           6          4         19         10        7
  XQ GAIN WILD-TYPE        20         17         59         43       54
                   vv
clus                STAGE IVA STAGE IVB
  XQ GAIN MUTATED           9         1
  XQ GAIN WILD-TYPE        18         1
D40V4, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 14                88
  STAGE IA                 0                 1
  STAGE II                 8                28
  STAGE IIA               24               147
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                6                20
  STAGE IIIA               4                17
  STAGE IIIB              19                59
  STAGE IIIC              10                43
  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  18  76   8
  XQ GAIN WILD-TYPE  18  87 336  57
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                18
  T2              18                87
  T3              76               336
  T4               8                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XQ GAIN MUTATED    51  30  21
  XQ GAIN WILD-TYPE 290 118  91
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              51               290
  N1              30               118
  N2              21                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  XQ GAIN MUTATED    74  12   3   1  12
  XQ GAIN WILD-TYPE 372  62   7   1  51
D40V7, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               74               372
  M1               12                62
  M1A               3                 7
  M1B               1                 1
  MX               12                51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    54  50
  XQ GAIN WILD-TYPE 229 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     54   50
  XQ GAIN WILD-TYPE  229  271
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              54               229
  MALE                50               271
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                     65                             8
  XQ GAIN WILD-TYPE                  313                            51
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                      29                              0
  XQ GAIN WILD-TYPE                   117                             13
D40V9, multiclass
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        65               313
  COLON MUCINOUS ADENOCARCINOMA                8                51
  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"
D40V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1 103
  XQ GAIN WILD-TYPE   8 492
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1  103
  XQ GAIN WILD-TYPE    8  492
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                1                 8
  YES             103               492
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    77   0   6   5
  XQ GAIN WILD-TYPE 359   5  30  24
D40V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              77               359
  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"
D40V12, 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                          13    52
  XQ GAIN WILD-TYPE                        43   240
D40V13, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                11
  BLACK OR AFRICAN AMERICAN                     13                43
  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(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   101  27
  1P LOSS WILD-TYPE 365  82
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              128               447 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27                82 
$`1P LOSS MUTATED`
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 
       43.76        35.11        36.53        14.53        32.45        29.19 
TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       23.61        22.52        21.76         5.03        38.99         9.07 
TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 
       37.05        19.99        50.04        37.05         0.99        38.99 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 
       37.02         0.99        33.07        32.05        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         1.58         1.02         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 
        0.43        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        61.87 
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 
        5.98         5.49        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         1.02        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-A032 
       36.03        25.97        23.01        12.00        70.03        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
        0.49         0.69        10.19         9.37         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       12.99        13.97        36.00        30.05       126.44       129.27 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
        0.49        20.55        15.85        11.97        14.86         1.02 
TCGA-F5-6813 TCGA-G5-6572 
        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 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        44.91        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        16.04        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        52.44         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-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         0.99 
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-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       36.95        14.93        17.03        36.03         0.99        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-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-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02        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        17.03 
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-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-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-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
       56.55         0.72         0.10         0.76         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        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        48.20        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         8.02        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 
       14.99        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         7.92        15.12        17.85         4.50        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         1.28         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        43.07        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 
        4.11        10.52         2.79         5.59         1.32         5.19 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        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         8.45        20.02        10.39        86.63 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
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-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       32.98         0.99         0.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       35.01        14.01        32.02        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
        0.99        20.98        13.94         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07         1.02        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-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.72         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97        13.97        60.03         7.99        10.98        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        15.02         7.10        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        2.40        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-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-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39         0.66         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.20              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27            140.38 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            17.13             17.95 
[1] "0.2 - 129.3 (17.1)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    90  44
  1P LOSS WILD-TYPE 348 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     90   44
  1P LOSS WILD-TYPE  348  118
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON               90               348
  RECTUM              44               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P LOSS MUTATED        17        0        5        34         1         0
  1P LOSS WILD-TYPE      85        1       31       137         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           6          4         18         17       22
  1P LOSS WILD-TYPE        20         17         60         36       39
                   vv
clus                STAGE IVA STAGE IVB
  1P LOSS MUTATED           4         0
  1P LOSS WILD-TYPE        23         2
D41V4, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 17                85
  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              18                60
  STAGE IIIC              17                36
  STAGE IV                22                39
  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  15
  1P LOSS WILD-TYPE  17  84 318  50
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               3                17
  T2              21                84
  T3              94               318
  T4              15                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    61  36  36
  1P LOSS WILD-TYPE 280 112  76
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              61               280
  N1              36               112
  N2              36                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  1P LOSS MUTATED    91  26   1   0  14
  1P LOSS WILD-TYPE 355  48   9   2  49
D41V7, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               91               355
  M1               26                48
  M1A               1                 9
  M1B               0                 2
  MX               14                49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    59  75
  1P LOSS WILD-TYPE 224 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     59   75
  1P LOSS WILD-TYPE  224  246
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              59               224
  MALE                75               246
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                     81                             9
  1P LOSS WILD-TYPE                  297                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                      43                              0
  1P LOSS WILD-TYPE                   103                             13
D41V9, multiclass
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        81               297
  COLON MUCINOUS ADENOCARCINOMA                9                50
  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"
D41V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3 131
  1P LOSS WILD-TYPE   6 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3  131
  1P LOSS WILD-TYPE    6  464
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                 6
  YES             131               464
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    89   1   9   5
  1P LOSS WILD-TYPE 347   4  27  24
D41V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              89               347
  R1               1                 4
  R2               9                27
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, 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                          15    66
  1P LOSS WILD-TYPE                        41   226
D41V13, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     15                41
  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(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    59  15
  1Q LOSS WILD-TYPE 407  94
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               74               501 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15                94 
$`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-3855 
       50.04         0.99        38.99        37.02        33.07        32.05 
TCGA-AA-3867 TCGA-AA-3966 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A02W 
       24.03         2.01         7.96        15.02        33.04        41.00 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4614 
        0.79         1.02         0.20         0.43        16.31         5.65 
TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CK-6748 
        5.13        29.56         5.23         3.19         2.14         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-D5-6531 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A285 
       11.08        10.06        17.75        13.41        11.38         6.12 
TCGA-DM-A28A TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       26.47         1.55         8.35        36.72        36.00        91.79 
TCGA-NH-A50U TCGA-NH-A8F8 TCGA-AF-2687 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 
       10.98         5.49        24.13        65.98        11.84         1.02 
TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
       24.00         1.02        19.99         1.02         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-BM-6198 
       19.99        36.03        25.97        23.01        12.00        10.19 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6511 TCGA-EI-7002 
        4.73        12.99        36.00         0.49        15.85        11.97 
TCGA-F5-6702 TCGA-G5-6572 
       14.86        47.08 

$`1Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 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-A6-6651 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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       13.02         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.99        36.03         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        17.03         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 
        0.99        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         1.58         0.10 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         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         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        75.25        50.37        58.39         1.41        32.94 
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-AZ-6608 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         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-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        48.20        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         8.02        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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        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         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        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         8.45        15.39        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-3593 TCGA-AG-3594 
        7.07         2.01         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-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       32.02        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98        13.94         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-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         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        1.81         6.05         6.05         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        15.02         7.10        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-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        31.30         0.39         1.02 
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-G5-6641 
       18.28        55.76        26.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.20              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.79            140.38 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           14.135            18.050 
[1] "0.2 - 91.8 (14.1)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    52  25
  1Q LOSS WILD-TYPE 386 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     52   25
  1Q LOSS WILD-TYPE  386  137
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON               52               386
  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        12        0        2        18         1         0
  1Q LOSS WILD-TYPE      90        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         71         45       47
                   vv
clus                STAGE IVA STAGE IVB
  1Q LOSS MUTATED           3         0
  1Q LOSS WILD-TYPE        24         2
D42V4, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 12                90
  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                71
  STAGE IIIC               8                45
  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  15  52   7
  1Q LOSS WILD-TYPE  18  90 360  58
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               2                18
  T2              15                90
  T3              52               360
  T4               7                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
  1Q LOSS MUTATED    36  21  19
  1Q LOSS WILD-TYPE 305 127  93
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              36               305
  N1              21               127
  N2              19                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  1Q LOSS MUTATED    49  16   1   0   9
  1Q LOSS WILD-TYPE 397  58   9   2  54
D42V7, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               49               397
  M1               16                58
  M1A               1                 9
  M1B               0                 2
  MX                9                54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    29  48
  1Q LOSS WILD-TYPE 254 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     29   48
  1Q LOSS WILD-TYPE  254  273
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              29               254
  MALE                48               273
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                     46                             6
  1Q LOSS WILD-TYPE                  332                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                      25                              0
  1Q LOSS WILD-TYPE                   121                             13
D42V9, multiclass
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        46               332
  COLON MUCINOUS ADENOCARCINOMA                6                53
  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"
D42V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  75
  1Q LOSS WILD-TYPE   7 520
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   75
  1Q LOSS WILD-TYPE    7  520
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2                 7
  YES              75               520
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    51   1   6   3
  1Q LOSS WILD-TYPE 385   4  30  26
D42V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              51               385
  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"
D42V12, 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                        45   257
D42V13, 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                45
  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(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    13   2
  2P LOSS WILD-TYPE 453 107
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               560 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               107 
$`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         1.02        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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 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        52.44         9.63         5.03         1.02         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-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-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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-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 
        0.99         0.99        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-3846 
       17.98        15.95        38.99        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-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 
       17.03         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         0.99 
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 
        1.58         1.02         0.10         0.76         0.20         0.43 
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         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        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 
       48.20        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         8.02        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        14.99        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 
        7.92        15.12        17.85         4.50        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         1.28         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        43.07        61.87        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         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        10.52         2.79         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        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-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
        8.45        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         8.02         7.07         2.01        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-4005 
       14.01         1.02        48.03        32.02        19.99        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-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04         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         4.60         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 
       60.03         7.99        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         7.10        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-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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        14.86         0.39         1.02         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 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.02              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            41.00            140.38 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           19.990            17.805 
[1] "1.0 - 41.0 (20.0)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6  11
  2P LOSS WILD-TYPE 432 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6   11
  2P LOSS WILD-TYPE  432  151
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON                6               432
  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     101        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         77         51       60
                   vv
clus                STAGE IVA STAGE IVB
  2P LOSS MUTATED           0         0
  2P LOSS WILD-TYPE        27         2
D43V4, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1               101
  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                77
  STAGE IIIC               2                51
  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  20 103 398  64
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3              14               398
  T4               1                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
  2P LOSS MUTATED    11   4   2
  2P LOSS WILD-TYPE 330 144 110
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              11               330
  N1               4               144
  N2               2               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  2P LOSS MUTATED    15   1   0   0   1
  2P LOSS WILD-TYPE 431  73  10   2  62
D43V7, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               15               431
  M1                1                73
  M1A               0                10
  M1B               0                 2
  MX                1                62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  10
  2P LOSS WILD-TYPE 276 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   10
  2P LOSS WILD-TYPE  276  311
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               276
  MALE                10               311
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                      6                             0
  2P LOSS WILD-TYPE                  372                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                       9                              1
  2P LOSS WILD-TYPE                   137                             12
D43V9, multiclass
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         6               372
  COLON MUCINOUS ADENOCARCINOMA                0                59
  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"
D43V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  16
  2P LOSS WILD-TYPE   8 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   16
  2P LOSS WILD-TYPE    8  579
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 8
  YES              16               579
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    14   0   1   0
  2P LOSS WILD-TYPE 422   5  35  29
D43V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              14               422
  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"
D43V12, 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                        56   289
D43V13, 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                56
  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(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    11   1
  2Q LOSS WILD-TYPE 455 108
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               563 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               108 
$`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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 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        52.44         9.63         5.03         1.02         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-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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        17.03 
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         0.99        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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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        48.20 
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         8.02        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        14.99        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         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        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         1.28         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        43.07        61.87        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         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        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         8.45 
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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        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         4.60 
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        60.03         7.99        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 
        7.10        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-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.01              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            41.00            140.38 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           27.005            17.750 
[1] "2.0 - 41.0 (27.0)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "2.1"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   7
  2Q LOSS WILD-TYPE 431 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    7
  2Q LOSS WILD-TYPE  431  155
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON                7               431
  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     101        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         78         51       61
                   vv
clus                STAGE IVA STAGE IVB
  2Q LOSS MUTATED           0         0
  2Q LOSS WILD-TYPE        27         2
D44V4, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1               101
  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                78
  STAGE IIIC               2                51
  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  20 103 401  64
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3              11               401
  T4               1                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
  2Q LOSS MUTATED    10   2   2
  2Q LOSS WILD-TYPE 331 146 110
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               331
  N1               2               146
  N2               2               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  2Q LOSS MUTATED    14   0   0   0   0
  2Q LOSS WILD-TYPE 432  74  10   2  63
D44V7, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               14               432
  M1                0                74
  M1A               0                10
  M1B               0                 2
  MX                0                63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   9
  2Q LOSS WILD-TYPE 278 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    9
  2Q LOSS WILD-TYPE  278  312
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5               278
  MALE                 9               312
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                      7                             0
  2Q LOSS WILD-TYPE                  371                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                       6                              0
  2Q LOSS WILD-TYPE                   140                             13
D44V9, multiclass
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         7               371
  COLON MUCINOUS ADENOCARCINOMA                0                59
  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"
D44V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  14
  2Q LOSS WILD-TYPE   9 581
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   14
  2Q LOSS WILD-TYPE    9  581
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 9
  YES              14               581
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   0
  2Q LOSS WILD-TYPE 423   5  36  29
D44V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               423
  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"
D44V12, 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                        56   291
D44V13, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               359 
       TCGA-3L-AA1B        TCGA-4T-AA8H        TCGA-A6-2671        TCGA-A6-2672 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676        TCGA-A6-2677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2682        TCGA-A6-2683        TCGA-A6-2684        TCGA-A6-2685 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2686        TCGA-A6-3807        TCGA-A6-3810        TCGA-A6-4105 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-4107        TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565        TCGA-A6-A566 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU        TCGA-AD-5900 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6895        TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6964        TCGA-AD-6965        TCGA-AD-A5EJ        TCGA-AD-A5EK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779        TCGA-AU-6004 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L        TCGA-AY-A69D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-A8YK        TCGA-AZ-4308        TCGA-AZ-4313        TCGA-AZ-4315 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-6715        TCGA-CA-6716 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951        TCGA-CK-4952 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750        TCGA-CM-4751 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280        TCGA-DM-A282 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6294 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298        TCGA-G4-6299 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6586 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6627 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6628        TCGA-NH-A50T        TCGA-NH-A50U        TCGA-NH-A50V 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A5IV        TCGA-NH-A6GA        TCGA-NH-A6GB        TCGA-NH-A6GC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A8F7        TCGA-NH-A8F8        TCGA-QG-A5YV        TCGA-QG-A5YX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5Z1        TCGA-QG-A5Z2        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(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    51  12
  3P LOSS WILD-TYPE 415  97
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               63               512 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                97 
$`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         0.99        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         0.43        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 
        7.92        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 
        5.98        26.99        30.28        12.72        14.50         2.01 
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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 
       13.94        15.52        37.05        37.25        16.04        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84        52.44         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         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         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        24.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        25.02        27.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-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         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        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        48.20        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 
        8.02        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        14.99 
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         4.50        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         1.28         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        43.07        61.87        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         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        10.52         2.79         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
        5.49        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39         8.45        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-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        7.07         1.02         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-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        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-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         1.81         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        60.03         7.99        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-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        30.05        12.95        10.06       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-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.20              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            85.05            140.38 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            12.72             19.02 
[1] "0.2 - 85.0 (12.7)"  "0.1 - 140.4 (19.0)"
[1] "hr=" "1.7"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    52  14
  3P LOSS WILD-TYPE 386 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     52   14
  3P LOSS WILD-TYPE  386  148
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON               52               386
  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      97        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         68         47       48
                   vv
clus                STAGE IVA STAGE IVB
  3P LOSS MUTATED           5         0
  3P LOSS WILD-TYPE        22         2
D45V4, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  5                97
  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                68
  STAGE IIIC               6                47
  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  18 101 360  56
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                18
  T2               4               101
  T3              52               360
  T4               9                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
  3P LOSS MUTATED    28  21  18
  3P LOSS WILD-TYPE 313 127  94
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              28               313
  N1              21               127
  N2              18                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  3P LOSS MUTATED    41  15   3   0   6
  3P LOSS WILD-TYPE 405  59   7   2  57
D45V7, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               41               405
  M1               15                59
  M1A               3                 7
  M1B               0                 2
  MX                6                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    28  39
  3P LOSS WILD-TYPE 255 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     28   39
  3P LOSS WILD-TYPE  255  282
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              28               255
  MALE                39               282
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                     48                             4
  3P LOSS WILD-TYPE                  330                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                      10                              3
  3P LOSS WILD-TYPE                   136                             10
D45V9, multiclass
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        48               330
  COLON MUCINOUS ADENOCARCINOMA                4                55
  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"
D45V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  65
  3P LOSS WILD-TYPE   7 530
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   65
  3P LOSS WILD-TYPE    7  530
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2                 7
  YES              65               530
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    46   0   8   4
  3P LOSS WILD-TYPE 390   5  28  25
D45V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              46               390
  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"
D45V12, 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                        50   260
D45V13, 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                50
  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(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    34   8
  3Q LOSS WILD-TYPE 432 101
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               533 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               101 
$`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         0.99 
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         0.43         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         7.92        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        26.99        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 
        2.01         1.02        10.19         6.05         5.29        18.28 

$`3Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        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-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-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       24.03        27.02        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-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-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         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         0.99        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         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        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 
       48.20        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         8.02        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        14.99        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 
        4.50        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         1.28         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        43.07        61.87        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         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
        5.49        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39         8.45        15.39        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-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        1.02        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-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        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-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-6620 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         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        60.03         7.99        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         7.10        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-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        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         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 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            85.05            140.38 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           12.855            18.250 
[1] "0.2 - 85.0 (12.9)"  "0.1 - 140.4 (18.2)"
[1] "hr=" "1.6"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    33   9
  3Q LOSS WILD-TYPE 405 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     33    9
  3Q LOSS WILD-TYPE  405  153
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON               33               405
  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      99        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         72         50       52
                   vv
clus                STAGE IVA STAGE IVB
  3Q LOSS MUTATED           3         0
  3Q LOSS WILD-TYPE        24         2
D46V4, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  3                99
  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                72
  STAGE IIIC               3                50
  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  20 102 378  59
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                20
  T2               3               102
  T3              34               378
  T4               6                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
  3Q LOSS MUTATED    21  11  11
  3Q LOSS WILD-TYPE 320 137 101
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              21               320
  N1              11               137
  N2              11               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  3Q LOSS MUTATED    26   9   2   0   4
  3Q LOSS WILD-TYPE 420  65   8   2  59
D46V7, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               26               420
  M1                9                65
  M1A               2                 8
  M1B               0                 2
  MX                4                59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    16  27
  3Q LOSS WILD-TYPE 267 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16   27
  3Q LOSS WILD-TYPE  267  294
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              16               267
  MALE                27               294
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                     30                             3
  3Q LOSS WILD-TYPE                  348                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                       5                              4
  3Q LOSS WILD-TYPE                   141                              9
D46V9, multiclass
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        30               348
  COLON MUCINOUS ADENOCARCINOMA                3                56
  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"
D46V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  41
  3Q LOSS WILD-TYPE   7 554
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   41
  3Q LOSS WILD-TYPE    7  554
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                 7
  YES              41               554
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    31   0   5   2
  3Q LOSS WILD-TYPE 405   5  31  27
D46V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              31               405
  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"
D46V12, 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                        51   272
D46V13, 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                51
  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(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   139  37
  4P LOSS WILD-TYPE 327  72
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              176               399 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               37                72 
$`4P LOSS MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       37.05        16.04        32.45        30.44        29.19        29.16 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       25.18        21.76        23.87        20.28        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 
        5.03         1.02        38.99        37.05        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 
       26.01        21.01        13.02        19.99         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 
       50.04        15.02        36.00        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       36.95        37.02        17.03         0.99        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 
       31.07        31.07        17.03        24.03        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 
       12.99        20.98         2.01        21.99        50.99        26.01 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       34.03        42.02        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 
       26.01         2.96        39.98         2.01        41.00         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        1.02         0.20        14.50         0.95        15.75         0.20 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
        5.52         5.65         5.13        65.00        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 
        3.19         2.14         3.29        48.20         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.03        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       15.02        13.05        11.08        11.01        10.06        14.99 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6924 TCGA-D5-6926 
       13.51        20.19        17.75         1.32        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       13.41        11.38        12.59       140.38         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
        6.12        14.04        26.47        16.24        33.67        35.41 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 
        8.35        23.51        45.11        36.72        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 
        4.11        10.98         5.49        26.99        24.13        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       43.04        12.72        37.74        14.50        15.39        65.98 
TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 
        1.02        34.03         6.05        19.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       32.98         1.02        35.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        36.03        14.04        13.94        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       12.00        70.03        41.00         0.69        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        6.05         4.73        12.99        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       30.05       126.44       129.27        32.61         2.40        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.34        16.41        11.97        31.30        14.86         0.39 
TCGA-F5-6813 TCGA-G5-6641 
        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 
        5.06         5.26        37.02        46.65        23.38        17.79 
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        52.44         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-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        29.00        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       37.05        19.00         5.03        26.99        19.04         0.99 
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-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        36.03        32.05        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00        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-3979 
       34.03        16.08        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-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         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         0.99        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-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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.43         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       16.31        21.44        17.82         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       50.37        58.39         1.41        32.94        83.80        22.36 
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-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.94         2.24         3.06         3.25         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-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-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
        8.02        26.04        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02         5.03        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       12.95        11.08        12.03        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         7.92        15.12        17.85         4.50 
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-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       10.13        12.43         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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91        13.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-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-F4-6809 
        6.18        35.87         1.55        16.31        29.59         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 
        0.53        19.43       107.67        28.21        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       13.78        35.80        26.17        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX 
        2.79         5.98         5.59         1.32         5.19        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 
        6.64        14.76        30.28        67.00        17.95        13.55 
TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       19.10        10.39         8.45        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
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-3894 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       14.01        32.02         1.02        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        38.04         0.49         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        11.01        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-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       17.00        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.20              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           140.38            139.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            17.13             17.95 
[1] "0.2 - 140.4 (17.1)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1.3"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   128  58
  4P LOSS WILD-TYPE 310 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    128   58
  4P LOSS WILD-TYPE  310  104
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON              128               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        25        0        5        49         2         0
  4P LOSS WILD-TYPE      77        1       31       122         8         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           7          9         24         21       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
D47V4, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 25                77
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               49               122
  STAGE IIB                2                 8
  STAGE IIC                0                 3
  STAGE III                7                19
  STAGE IIIA               9                12
  STAGE IIIB              24                54
  STAGE IIIC              21                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  29 130  23
  4P LOSS WILD-TYPE  14  76 282  42
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               6                14
  T2              29                76
  T3             130               282
  T4              23                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    87  55  46
  4P LOSS WILD-TYPE 254  93  66
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              87               254
  N1              55                93
  N2              46                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  4P LOSS MUTATED   124  35   5   1  18
  4P LOSS WILD-TYPE 322  39   5   1  45
D47V7, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              124               322
  M1               35                39
  M1A               5                 5
  M1B               1                 1
  MX               18                45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    86 102
  4P LOSS WILD-TYPE 197 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     86  102
  4P LOSS WILD-TYPE  197  219
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              86               197
  MALE               102               219
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                    119                             9
  4P LOSS WILD-TYPE                  259                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                      54                              3
  4P LOSS WILD-TYPE                    92                             10
D47V9, multiclass
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       119               259
  COLON MUCINOUS ADENOCARCINOMA                9                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"
D47V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     8 180
  4P LOSS WILD-TYPE   1 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8  180
  4P LOSS WILD-TYPE    1  415
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                8                 1
  YES             180               415
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   135   0  15   6
  4P LOSS WILD-TYPE 301   5  21  23
D47V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             135               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"
D47V12, 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                          17    90
  4P LOSS WILD-TYPE                        39   202
D47V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     17                39
  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(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   138  33
  4Q LOSS WILD-TYPE 328  76
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              171               404 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               33                76 
$`4Q LOSS MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       43.76        43.43        35.11        13.94        15.52        37.05 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 
       32.45        29.19        29.16        21.76        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
       61.84         9.63         5.03        38.99        37.05        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 
       29.00        26.01        33.99        21.01        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
        6.05         2.01        50.04        37.05        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
        0.99        38.99        36.95        37.02        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 
       33.07         0.99        31.07        17.03         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00F 
        2.01        21.99        50.99        26.01        24.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       42.02        15.02        32.02        33.04        26.01         2.96 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       39.98        41.00         1.58         1.02         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
       16.31         0.95         0.20         5.52         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-6719 TCGA-CK-5912 
       65.00        12.10        29.56         2.14         1.35        48.20 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.08        11.01        14.99        13.51        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D9 TCGA-DM-A1DA 
        1.32         7.92         9.04        13.41       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6807 
       44.32         6.12        14.04        26.47        13.38        16.24 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
       35.41         8.35        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV 
       46.75         4.11        10.98         5.98         5.49        26.99 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        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         1.02        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 
        6.05        19.99        29.98        32.98         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 
       48.03        19.99        28.04        36.03        14.04        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X 
       25.97        23.01        12.00        70.03        64.01        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
        0.49         0.69        10.19         6.05         6.05         4.73 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       11.01        12.99        15.02        36.00         7.10        30.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
      126.44       129.27         2.40        17.00        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       16.41        11.97        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        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 
        5.06         5.26        37.02        46.65        23.38        17.79 
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        16.04        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 
       52.44         1.02         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-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 
       19.07        29.00        12.99         0.99        14.01        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-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3854 
       25.02         1.02        17.98        15.95        14.93        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       32.05        31.07        53.00        24.03        27.02        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-3971 TCGA-AA-3973 TCGA-AA-3975 
       24.00         2.01        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
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-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02         0.99        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-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         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
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-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77       100.01         5.23        11.74         3.19         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-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-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         8.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       12.26        19.59        11.51        20.42        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        7.53        12.39        10.13        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       12.59       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        33.67         1.28         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        82.39        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.59         1.32         5.19        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       30.28        67.00        17.95        10.39         8.45        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         2.01        24.00         1.02        46.03 
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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99         1.02         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
       36.95        17.03        13.02        35.01        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-A020 
       15.95        36.03         9.07         1.02        31.00        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-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 
        1.45         0.72         4.60         1.81         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03         7.99        10.98        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       13.97        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       19.96        20.91        18.28        17.69        16.31         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-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       37.51         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.20              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.38            139.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           17.030            18.015 
[1] "0.2 - 140.4 (17.0)" "0.1 - 139.2 (18.0)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   116  62
  4Q LOSS WILD-TYPE 322 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    116   62
  4Q LOSS WILD-TYPE  322  100
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON              116               322
  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        24        0        6        49         1         0
  4Q LOSS WILD-TYPE      78        1       30       122         9         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           7          8         26         24       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
D48V4, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 24                78
  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              26                52
  STAGE IIIC              24                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  28 126  23
  4Q LOSS WILD-TYPE  15  77 286  42
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                15
  T2              28                77
  T3             126               286
  T4              23                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  55  42
  4Q LOSS WILD-TYPE 256  93  70
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              85               256
  N1              55                93
  N2              42                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  4Q LOSS MUTATED   125  28   5   0  21
  4Q LOSS WILD-TYPE 321  46   5   2  42
D48V7, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              125               321
  M1               28                46
  M1A               5                 5
  M1B               0                 2
  MX               21                42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    83  99
  4Q LOSS WILD-TYPE 200 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     83   99
  4Q LOSS WILD-TYPE  200  222
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              83               200
  MALE                99               222
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                    106                            10
  4Q LOSS WILD-TYPE                  272                            49
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                      58                              3
  4Q LOSS WILD-TYPE                    88                             10
D48V9, multiclass
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       106               272
  COLON MUCINOUS ADENOCARCINOMA               10                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"
D48V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 174
  4Q LOSS WILD-TYPE   1 421
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  174
  4Q LOSS WILD-TYPE    1  421
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                8                 1
  YES             174               421
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   131   1  11   7
  4Q LOSS WILD-TYPE 305   4  25  22
D48V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             131               305
  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"
D48V12, 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                          18    91
  4Q LOSS WILD-TYPE                        38   201
D48V13, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     18                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(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    59  17
  5P LOSS WILD-TYPE 407  92
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               76               499 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17                92 
$`5P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-3810 TCGA-A6-4105 
       37.02        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         0.99        36.95 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00F 
        0.99        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         0.99        33.04        41.00         1.02 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 
        0.20        16.31         5.65        65.00        62.79         5.23 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       48.20         8.02        29.06        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 
       14.04        29.03        11.01        17.85        10.13        12.43 
TCGA-D5-6926 TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV 
        9.04         8.35        36.00         4.11        10.98        26.99 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 
       24.13        43.04        15.39         6.05         1.02        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A01W TCGA-CI-6620 
        1.02        48.03        28.04        23.01        70.03         6.05 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-EI-6506 
       13.97        36.00         7.10       126.44        57.24        20.55 
TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7004 TCGA-G5-6233 
       16.41        13.64         8.45        18.28 

$`5P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        34.65        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        29.16        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-A6-6780 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        52.44         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-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-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-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         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3856 
       38.99        37.02        14.93        17.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        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-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-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-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         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       13.02        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        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        14.99 
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-D5-6537 
       17.75        18.25         1.32         7.92        15.12         4.50 
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-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         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         1.28         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 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       30.28        67.00        17.95        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         8.45        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         1.02         2.01        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         4.60 
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        60.03         7.99        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        14.86         0.39         1.02         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 
             0.20              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            140.38 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            21.29             17.56 
[1] "0.2 - 126.4 (21.3)" "0.1 - 140.4 (17.6)"
[1] "hr=" "1.2"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    55  27
  5P LOSS WILD-TYPE 383 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     55   27
  5P LOSS WILD-TYPE  383  135
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON               55               383
  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        13        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         67         42       54
                   vv
clus                STAGE IVA STAGE IVB
  5P LOSS MUTATED           8         0
  5P LOSS WILD-TYPE        19         2
D49V4, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 13                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                67
  STAGE IIIC              11                42
  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  13  55  11
  5P LOSS WILD-TYPE  17  92 357  54
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               3                17
  T2              13                92
  T3              55               357
  T4              11                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P LOSS MUTATED    35  27  20
  5P LOSS WILD-TYPE 306 121  92
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              35               306
  N1              27               121
  N2              20                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  5P LOSS MUTATED    58  10   4   0  10
  5P LOSS WILD-TYPE 388  64   6   2  53
D49V7, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               58               388
  M1               10                64
  M1A               4                 6
  M1B               0                 2
  MX               10                53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    41  41
  5P LOSS WILD-TYPE 242 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     41   41
  5P LOSS WILD-TYPE  242  280
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              41               242
  MALE                41               280
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                     50                             5
  5P LOSS WILD-TYPE                  328                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                      26                              1
  5P LOSS WILD-TYPE                   120                             12
D49V9, multiclass
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        50               328
  COLON MUCINOUS ADENOCARCINOMA                5                54
  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"
D49V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4  78
  5P LOSS WILD-TYPE   5 517
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   78
  5P LOSS WILD-TYPE    5  517
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4                 5
  YES              78               517
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    56   1   3   3
  5P LOSS WILD-TYPE 380   4  33  26
D49V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              56               380
  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"
D49V12, 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                           7    47
  5P LOSS WILD-TYPE                        49   245
D49V13, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      7                49
  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(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    80  29
  5Q LOSS WILD-TYPE 386  80
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              109               466 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               29                80 
$`5Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       37.02        43.76        13.94        16.04        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         0.99        36.95         0.99 
TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00F 
       33.07        31.07        24.03        24.00         2.01        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02H TCGA-AA-A02W 
       27.02        42.02         0.99        33.04         2.01        41.00 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 
        1.02         0.10         0.20        16.31         0.20         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 
       65.00        62.79         5.23         1.94         3.29         1.35 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       48.20         8.02        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       29.03        13.02        17.85        10.13        12.43         9.04 
TCGA-D5-6929 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 
       13.41        44.32         6.12         8.61         1.55         8.35 
TCGA-G4-6297 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV 
       82.39        36.00        91.79         4.11        10.98        26.99 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 
       30.28        24.13        17.23        43.04        37.74        15.39 
TCGA-AF-A56K TCGA-AG-3578 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 
       86.63        32.02        29.98         1.02        32.98        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y 
        1.02        48.03        28.04        36.03        17.03        23.01 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-BM-6198 TCGA-CI-6620 
       70.03        64.01         1.94        38.96        10.19         6.05 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.99        13.97        15.02        36.00         7.10        13.05 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-F5-6702 
      126.44        57.24        51.48        20.55        16.41        14.86 
TCGA-G5-6233 
       18.28 

$`5Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
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        15.52        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-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        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-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        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-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 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 
       15.95        38.99        37.02        14.93        17.03        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       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-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-A02J 
       37.02        39.06        51.98         2.96        39.98         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         1.58 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        75.25        50.37        58.39         1.41        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-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01        29.56        11.74         3.19         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-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         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        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 
       14.99        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         7.92        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 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         1.28 
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        43.07        61.87        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-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       67.00        17.95        13.55        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N 
       14.50         8.45        20.02        10.39        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07         1.02         2.01 
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-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         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-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-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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       12.00        31.00        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        4.60         1.81         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        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       12.00        30.05        12.95        10.06         5.29        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.97         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            140.38 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.99             17.72 
[1] "0.1 - 126.4 (20.0)" "0.1 - 140.4 (17.7)"
[1] "hr=" "1.5"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    75  41
  5Q LOSS WILD-TYPE 363 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     75   41
  5Q LOSS WILD-TYPE  363  121
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON               75               363
  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        15        0        6        26         0         1
  5Q LOSS WILD-TYPE      87        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         63         36       48
                   vv
clus                STAGE IVA STAGE IVB
  5Q LOSS MUTATED          10         0
  5Q LOSS WILD-TYPE        17         2
D50V4, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 15                87
  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                63
  STAGE IIIC              17                36
  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  16  85  12
  5Q LOSS WILD-TYPE  17  89 327  53
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               3                17
  T2              16                89
  T3              85               327
  T4              12                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
  5Q LOSS MUTATED    52  31  33
  5Q LOSS WILD-TYPE 289 117  79
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              52               289
  N1              31               117
  N2              33                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  5Q LOSS MUTATED    77  18   5   0  14
  5Q LOSS WILD-TYPE 369  56   5   2  49
D50V7, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               77               369
  M1               18                56
  M1A               5                 5
  M1B               0                 2
  MX               14                49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    51  65
  5Q LOSS WILD-TYPE 232 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     51   65
  5Q LOSS WILD-TYPE  232  256
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              51               232
  MALE                65               256
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                     68                             7
  5Q LOSS WILD-TYPE                  310                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                      39                              1
  5Q LOSS WILD-TYPE                   107                             12
D50V9, multiclass
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        68               310
  COLON MUCINOUS ADENOCARCINOMA                7                52
  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"
D50V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     6 110
  5Q LOSS WILD-TYPE   3 485
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6  110
  5Q LOSS WILD-TYPE    3  485
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                6                 3
  YES             110               485
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    78   2   7   4
  5Q LOSS WILD-TYPE 358   3  29  25
D50V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              78               358
  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"
D50V12, 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                          11    59
  5Q LOSS WILD-TYPE                        45   233
D50V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                     11                45
  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(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    30  12
  6P LOSS WILD-TYPE 436  97
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               42               533 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12                97 
$`6P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3561 
       37.02        42.28        16.04        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         0.99        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         1.58 
TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        0.43         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        14.99        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-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        44.91        35.11        45.60        13.94        15.52 
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-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
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-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-3562 
       17.95        29.95        23.01        20.98        19.99        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-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         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        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-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         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 
        0.99        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-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-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.02         0.10         0.76         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-A8YK TCGA-AZ-4308 
       21.44        17.82         5.19         5.52         6.87        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 
       48.20        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         8.02        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         7.92        15.12        17.85         4.50        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         1.28         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 
       43.07        61.87        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50         8.45        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         1.02         2.01        24.00         1.02        46.03 
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-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-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         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        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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         7.10        30.05        12.95 
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-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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.43              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            42.28            140.38 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.94             18.05 
[1] "0.4 - 42.3 (13.9)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "2.4"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    33  11
  6P LOSS WILD-TYPE 405 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33   11
  6P LOSS WILD-TYPE  405  151
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON               33               405
  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      95        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         75         50       58
                   vv
clus                STAGE IVA STAGE IVB
  6P LOSS MUTATED           3         0
  6P LOSS WILD-TYPE        24         2
D51V4, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  7                95
  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                75
  STAGE IIIC               3                50
  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  99 382  58
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                18
  T2               6                99
  T3              30               382
  T4               7                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
  6P LOSS MUTATED    31   8   6
  6P LOSS WILD-TYPE 310 140 106
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              31               310
  N1               8               140
  N2               6               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  6P LOSS MUTATED    34   4   2   0   5
  6P LOSS WILD-TYPE 412  70   8   2  58
D51V7, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               34               412
  M1                4                70
  M1A               2                 8
  M1B               0                 2
  MX                5                58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    19  26
  6P LOSS WILD-TYPE 264 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     19   26
  6P LOSS WILD-TYPE  264  295
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              19               264
  MALE                26               295
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                     28                             5
  6P LOSS WILD-TYPE                  350                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                       8                              3
  6P LOSS WILD-TYPE                   138                             10
D51V9, multiclass
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        28               350
  COLON MUCINOUS ADENOCARCINOMA                5                54
  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"
D51V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  44
  6P LOSS WILD-TYPE   8 551
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   44
  6P LOSS WILD-TYPE    8  551
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 8
  YES              44               551
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    31   0   1   6
  6P LOSS WILD-TYPE 405   5  35  23
D51V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              31               405
  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"
D51V12, 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                        55   269
D51V13, 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                55
  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(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    49  15
  6Q LOSS WILD-TYPE 417  94
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               64               511 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15                94 
$`6Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-4107 TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3552 
       37.02        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         0.99        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         0.99        26.01         2.01 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        1.58         0.43         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        14.99 
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         5.98        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-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        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-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
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-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-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        19.99        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-3811 
       19.00         5.03        85.05        26.99        19.04         0.99 
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-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        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-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       27.02        31.00         2.01        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-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         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-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-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         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         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         0.20         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        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        48.20 
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         8.02        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         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        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         1.28         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        43.07        61.87        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         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       24.13        17.95        37.74        10.39        14.50         8.45 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       36.03         8.02         7.07         1.02         2.01         1.02 
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-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        36.03         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         1.45         0.69         0.72         4.60 
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        60.03         7.99        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-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        30.05        12.95        10.06       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-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        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 
       47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.43              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            61.02            140.38 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.94             18.05 
[1] "0.4 - 61.0 (13.9)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.8"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    45  21
  6Q LOSS WILD-TYPE 393 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     45   21
  6Q LOSS WILD-TYPE  393  141
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON               45               393
  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      92        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         71         44       54
                   vv
clus                STAGE IVA STAGE IVB
  6Q LOSS MUTATED           3         1
  6Q LOSS WILD-TYPE        24         1
D52V4, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 10                92
  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                71
  STAGE IIIC               9                44
  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  97 364  57
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               4                16
  T2               8                97
  T3              48               364
  T4               8                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
  6Q LOSS MUTATED    36  13  19
  6Q LOSS WILD-TYPE 305 135  93
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              36               305
  N1              13               135
  N2              19                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  6Q LOSS MUTATED    46   9   2   1  10
  6Q LOSS WILD-TYPE 400  65   8   1  53
D52V7, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               46               400
  M1                9                65
  M1A               2                 8
  M1B               1                 1
  MX               10                53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    27  41
  6Q LOSS WILD-TYPE 256 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27   41
  6Q LOSS WILD-TYPE  256  280
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              27               256
  MALE                41               280
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                     38                             7
  6Q LOSS WILD-TYPE                  340                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                      16                              5
  6Q LOSS WILD-TYPE                   130                              8
D52V9, multiclass
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        38               340
  COLON MUCINOUS ADENOCARCINOMA                7                52
  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"
D52V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  67
  6Q LOSS WILD-TYPE   8 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   67
  6Q LOSS WILD-TYPE    8  528
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 8
  YES              67               528
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    50   0   3   7
  6Q LOSS WILD-TYPE 386   5  33  22
D52V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              50               386
  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"
D52V12, 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                        53   263
D52V13, 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                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(53) Variable = 7Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 463 109
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               572 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0               109 
$`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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 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        52.44         9.63         5.03         1.02         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-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-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-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         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
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        17.03 
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         0.99        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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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 
       48.20        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         8.02        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        14.99        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         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        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         1.28         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 
       43.07        61.87        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        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         8.45        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         1.02         2.01 
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-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-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         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         4.60         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        60.03         7.99 
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         7.10        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-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            11.38              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            29.06            140.38 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.940            17.835 
[1] "11.4 - 29.1 (13.9)" "0.1 - 140.4 (17.8)"
[1] "hr="     "3300000"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   2
  7Q LOSS WILD-TYPE 436 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    2
  7Q LOSS WILD-TYPE  436  160
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON                2               436
  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     101        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         78         53       61
                   vv
clus                STAGE IVA STAGE IVB
  7Q LOSS MUTATED           0         0
  7Q LOSS WILD-TYPE        27         2
D53V4, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1               101
  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                78
  STAGE IIIC               0                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
  7Q LOSS MUTATED     0   2   2   0
  7Q LOSS WILD-TYPE  20 103 410  65
D53V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3               2               410
  T4               0                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
  7Q LOSS MUTATED     3   1   0
  7Q LOSS WILD-TYPE 338 147 112
D53V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               3               338
  N1               1               147
  N2               0               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  7Q LOSS MUTATED     4   0   0   0   0
  7Q LOSS WILD-TYPE 442  74  10   2  63
D53V7, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0                4               442
  M1                0                74
  M1A               0                10
  M1B               0                 2
  MX                0                63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   1
  7Q LOSS WILD-TYPE 280 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE  280  320
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3               280
  MALE                 1               320
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                      2                             0
  7Q LOSS WILD-TYPE                  376                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                       1                              1
  7Q LOSS WILD-TYPE                   145                             12
D53V9, multiclass
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         2               376
  COLON MUCINOUS ADENOCARCINOMA                0                59
  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"
D53V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   4
  7Q LOSS WILD-TYPE   9 591
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    4
  7Q LOSS WILD-TYPE    9  591
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 9
  YES               4               591
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     4   0   0   0
  7Q LOSS WILD-TYPE 432   5  36  29
D53V11, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               4               432
  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"
D53V12, 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                        56   290
D53V13, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               359 
       TCGA-3L-AA1B        TCGA-4T-AA8H        TCGA-A6-2671        TCGA-A6-2672 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676        TCGA-A6-2677 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2681 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2682        TCGA-A6-2683        TCGA-A6-2684        TCGA-A6-2685 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-2686        TCGA-A6-3807        TCGA-A6-3810        TCGA-A6-4105 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-4107        TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565        TCGA-A6-A566 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU        TCGA-AD-5900 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-6895        TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AD-6964        TCGA-AD-6965        TCGA-AD-A5EJ        TCGA-AD-A5EK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779        TCGA-AU-6004 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L        TCGA-AY-A69D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AY-A8YK        TCGA-AZ-4308        TCGA-AZ-4313        TCGA-AZ-4315 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5344        TCGA-CM-5348 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-7000 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A280        TCGA-DM-A282        TCGA-DM-A285 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C        TCGA-DM-A28E 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H        TCGA-DM-A28K 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6461 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6294        TCGA-G4-6295 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6297        TCGA-G4-6298        TCGA-G4-6299        TCGA-G4-6302 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6311        TCGA-G4-6314 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320        TCGA-G4-6321 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6586        TCGA-G4-6588 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6627        TCGA-G4-6628 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-NH-A50T        TCGA-NH-A50U        TCGA-NH-A50V        TCGA-NH-A5IV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-NH-A6GA        TCGA-NH-A6GB        TCGA-NH-A6GC        TCGA-NH-A8F7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-NH-A8F8        TCGA-QG-A5YV        TCGA-QG-A5YX        TCGA-QG-A5Z1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-QG-A5Z2        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(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   165  41
  8P LOSS WILD-TYPE 301  68
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              206               369 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41                68 
$`8P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
       45.60        15.52        34.65        36.53        32.91        30.44 
TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       23.61        27.09        24.13        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       24.69        23.87        20.28        61.84        52.44         5.03 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3538 
       37.05         1.02        38.99        24.03        34.03        26.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       19.99        78.08         2.01        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 
        5.98        37.05        19.00        36.00        85.05        37.02 
TCGA-AA-3851 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 
       33.07        31.07        17.03        24.03        27.02         2.01 
TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       24.00        34.03        16.08        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A017 TCGA-AA-A01G 
       27.02         7.96        19.00        34.03        15.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02W TCGA-AD-6901 
       31.00         1.02        33.04        37.02        41.00         1.02 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 
        0.20        16.31        15.75         0.20         5.52        75.25 
TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
        5.65        83.80        62.79        12.10        29.56        11.74 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4752 TCGA-CM-5344 
        1.94         3.29         1.35        15.62        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6166 
       22.98        30.08        16.01         5.03        14.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 
       13.02        15.02        13.05        11.08        10.06        12.26 
TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6922 
       13.51         7.92        15.12        12.49        15.58        10.13 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
        9.04        13.41        11.38       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28G TCGA-F4-6460 
      140.38       131.51         6.12        26.47        60.79        13.38 
TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6298 TCGA-G4-6299 
       13.64         1.55        16.31         0.53        23.51        74.56 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-NH-A50U 
       35.93        36.72        36.00        26.43        91.79        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 
       10.52         5.98         5.49        30.28        17.95        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 
       13.55        19.10        37.74        10.39        15.39        10.39 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        1.02        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
        6.05         0.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3909 TCGA-AG-3999 
        0.99         1.02        17.03        35.01        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       36.03        14.04        17.03        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       15.95         1.02        12.00        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 
       38.96        41.00         1.45         0.72        10.19         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       13.97        60.03        10.98        11.01        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       36.00         7.10        10.06         5.29       126.44       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 
       51.48         2.40        15.85        16.34        10.78        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
        8.45         9.96        31.30        14.86         0.69         0.46 
TCGA-G5-6233 TCGA-G5-6641 
       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 
        5.06         5.26        46.65        23.38        17.79        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5657 
       37.05        37.25        16.04        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         1.02         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         0.99         0.99 
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-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        36.95        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
       20.98         2.01        21.99        50.99        13.05        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       32.02        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        21.44        17.82         5.19 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
        6.87        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        61.41        49.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23         3.19         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        48.20        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-5341 TCGA-CM-5861 
        8.02        26.04         8.02        27.02        29.06        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.01        12.03        14.99        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       20.19        20.42        17.75        18.25         1.32        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.50        17.13        16.14         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
      119.70        24.43        38.20        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.45         6.18        35.87        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 
       55.04        51.75        45.11        39.42        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
        4.11         2.79         5.59         1.32         5.19        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 
       17.29         6.64        14.76        67.00        24.13        43.04 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       12.72        14.50         8.45        20.02        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-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
        2.01        50.04        12.03        15.95        19.99        19.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
        1.02        48.03        32.02         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
       13.94         6.02        36.03         9.07        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       64.01        49.97        61.97        38.04         0.49         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
        7.99        15.02        12.00        15.02        30.05        12.95 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       13.05        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        13.64        17.46 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       37.51         0.39         1.02         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.20              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           140.38            139.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           18.115            17.790 
[1] "0.2 - 140.4 (18.1)" "0.1 - 139.2 (17.8)"
[1] "hr=" "1.1"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   138  73
  8P LOSS WILD-TYPE 300  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    138   73
  8P LOSS WILD-TYPE  300   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON              138               300
  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        28        0        9        51         2         1
  8P LOSS WILD-TYPE      74        1       27       120         8         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED          12         10         27         24       31
  8P LOSS WILD-TYPE        14         11         51         29       30
                   vv
clus                STAGE IVA STAGE IVB
  8P LOSS MUTATED          12         1
  8P LOSS WILD-TYPE        15         1
D54V4, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 28                74
  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              27                51
  STAGE IIIC              24                29
  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  33 154  23
  8P LOSS WILD-TYPE  17  72 258  42
D54V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                17
  T2              33                72
  T3             154               258
  T4              23                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    98  60  54
  8P LOSS WILD-TYPE 243  88  58
D54V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              98               243
  N1              60                88
  N2              54                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  8P LOSS MUTATED   147  36   5   1  21
  8P LOSS WILD-TYPE 299  38   5   1  42
D54V7, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              147               299
  M1               36                38
  M1A               5                 5
  M1B               1                 1
  MX               21                42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    90 123
  8P LOSS WILD-TYPE 193 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     90  123
  8P LOSS WILD-TYPE  193  198
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              90               193
  MALE               123               198
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                    125                            12
  8P LOSS WILD-TYPE                  253                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                      67                              5
  8P LOSS WILD-TYPE                    79                              8
D54V9, multiclass
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       125               253
  COLON MUCINOUS ADENOCARCINOMA               12                47
  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"
D54V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5 208
  8P LOSS WILD-TYPE   4 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  208
  8P LOSS WILD-TYPE    4  387
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                5                 4
  YES             208               387
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   152   2  16   5
  8P LOSS WILD-TYPE 284   3  20  24
D54V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             152               284
  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"
D54V12, 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                          21   100
  8P LOSS WILD-TYPE                        35   192
D54V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 9
  BLACK OR AFRICAN AMERICAN                     21                35
  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(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27   7
  8Q LOSS WILD-TYPE 439 102
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               541 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               102 
$`8Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-6782 
       37.02        43.76        44.91        15.52        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         1.02 
TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6679 
        0.20         0.20         5.52        62.79        16.01        10.06 
TCGA-D5-5538 TCGA-D5-6539 TCGA-DM-A1D6 TCGA-F4-6704 TCGA-G4-6625 TCGA-AG-3883 
       12.26        12.49        49.91         1.55        91.79         1.02 
TCGA-AG-3890 TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6644 TCGA-DC-6157 
       17.03        23.01        12.00        41.00         0.72        36.00 
TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 TCGA-G5-6233 
       51.48        15.85         0.69        18.28 

$`8Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        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-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        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 
       37.05        36.03         8.05        19.07        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-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-3994 TCGA-AA-A004 
       25.02        24.00        27.02        19.07        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 
       17.03         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         0.99 
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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         6.87        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        48.20        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 
        8.02        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        14.99        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         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        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 
        1.28         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        43.07        61.87 
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 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       14.76        30.28        67.00        24.13        17.95        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         8.45        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         1.02         2.01        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-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-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        0.99        20.98        13.94         6.02        25.97        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-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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        38.04         0.49         1.45         0.69         4.60 
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        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       15.02        12.99        12.00        13.97        15.02         7.10 
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-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        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-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
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 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.20              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.79            140.38 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           17.655            17.820 
[1] "0.2 - 91.8 (17.7)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    23  12
  8Q LOSS WILD-TYPE 415 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     23   12
  8Q LOSS WILD-TYPE  415  150
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON               23               415
  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         4        0        1        10         2         1
  8Q LOSS WILD-TYPE      98        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         75         49       57
                   vv
clus                STAGE IVA STAGE IVB
  8Q LOSS MUTATED           2         0
  8Q LOSS WILD-TYPE        25         2
D55V4, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  4                98
  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                75
  STAGE IIIC               4                49
  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   4  26   5
  8Q LOSS WILD-TYPE  20 101 386  60
D55V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                20
  T2               4               101
  T3              26               386
  T4               5                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
  8Q LOSS MUTATED    20   5   9
  8Q LOSS WILD-TYPE 321 143 103
D55V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              20               321
  N1               5               143
  N2               9               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"
                   vv
clus                 M0  M1 M1A M1B  MX
  8Q LOSS MUTATED    21   5   1   0   6
  8Q LOSS WILD-TYPE 425  69   9   2  57
D55V7, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               21               425
  M1                5                69
  M1A               1                 9
  M1B               0                 2
  MX                6                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     9  26
  8Q LOSS WILD-TYPE 274 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9   26
  8Q LOSS WILD-TYPE  274  295
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               9               274
  MALE                26               295
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                     19                             4
  8Q LOSS WILD-TYPE                  359                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                      12                              0
  8Q LOSS WILD-TYPE                   134                             13
D55V9, multiclass
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        19               359
  COLON MUCINOUS ADENOCARCINOMA                4                55
  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"
D55V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  35
  8Q LOSS WILD-TYPE   9 560
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   35
  8Q LOSS WILD-TYPE    9  560
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 9
  YES              35               560
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    27   0   1   0
  8Q LOSS WILD-TYPE 409   5  35  29
D55V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              27               409
  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"
D55V12, 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                           2    21
  8Q LOSS WILD-TYPE                        54   271
D55V13, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                12
  BLACK OR AFRICAN AMERICAN                      2                54
  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(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    57  13
  9P LOSS WILD-TYPE 409  96
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               70               505 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                96 
$`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         7.92         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         5.98         5.49 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 
       24.13        13.55        65.98         2.01        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         7.10 
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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        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-A6-4107 
       15.52        37.05        37.25        16.04        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-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-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        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-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-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-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-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        17.03         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         0.99        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-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        1.58         1.02         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        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        48.20        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         8.02        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 
       14.99        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         4.50        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         1.28         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        43.07        61.87 
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         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       30.28        67.00        17.95        17.23        43.04        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         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03         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-3732 
       19.99        19.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07         1.02        70.03        64.01        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         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97         9.37        60.03         7.99        10.98 
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-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-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        24.13        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-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 
       14.86         0.39         1.02         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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            85.05            140.38 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           14.515            18.050 
[1] "0.2 - 85.0 (14.5)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    51  22
  9P LOSS WILD-TYPE 387 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51   22
  9P LOSS WILD-TYPE  387  140
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON               51               387
  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      89        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         69         45       48
                   vv
clus                STAGE IVA STAGE IVB
  9P LOSS MUTATED           4         0
  9P LOSS WILD-TYPE        23         2
D56V4, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 13                89
  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                69
  STAGE IIIC               8                45
  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  88 370  52
D56V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                18
  T2              17                88
  T3              42               370
  T4              13                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
  9P LOSS MUTATED    37  18  18
  9P LOSS WILD-TYPE 304 130  94
D56V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              37               304
  N1              18               130
  N2              18                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  9P LOSS MUTATED    51  15   2   0   6
  9P LOSS WILD-TYPE 395  59   8   2  57
D56V7, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               51               395
  M1               15                59
  M1A               2                 8
  M1B               0                 2
  MX                6                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  45
  9P LOSS WILD-TYPE 254 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   45
  9P LOSS WILD-TYPE  254  276
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29               254
  MALE                45               276
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                     49                             2
  9P LOSS WILD-TYPE                  329                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                      21                              1
  9P LOSS WILD-TYPE                   125                             12
D56V9, multiclass
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        49               329
  COLON MUCINOUS ADENOCARCINOMA                2                57
  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"
D56V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  73
  9P LOSS WILD-TYPE   8 522
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   73
  9P LOSS WILD-TYPE    8  522
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 8
  YES              73               522
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    47   2   8   3
  9P LOSS WILD-TYPE 389   3  28  26
D56V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              47               389
  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"
D56V12, 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                        50   255
D56V13, 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                50
  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(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    55  15
  9Q LOSS WILD-TYPE 411  94
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               70               505 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               15                94 
$`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-5344 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
        0.26         8.02        22.03        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6898 TCGA-DM-A0XF 
       11.01        10.06        20.19         1.32         7.53        38.20 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-NH-A6GA TCGA-NH-A8F8 
       33.67         8.35        82.39        61.87         5.98         5.49 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3731 
       24.13        13.55        65.98         2.01        34.03         1.02 
TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 
       19.99        36.03        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         7.10 
TCGA-DC-6160 TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6702 
       30.05         0.49        16.31        14.86 

$`9Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        23.38        17.79 
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        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        16.04        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-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         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-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        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-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        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-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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-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-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
        0.20         0.43         0.46         0.92        27.09        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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        48.20 
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         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        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 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24         1.28         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        43.07 
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         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       30.28        67.00        17.95        17.23        43.04        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         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-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-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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07         1.02        70.03        64.01        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         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97         9.37        60.03         7.99        10.98 
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-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-5831 
       57.24       129.27        24.13        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        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-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39         1.02         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 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            85.05            140.38 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            16.31             17.85 
[1] "0.3 - 85.0 (16.3)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    50  22
  9Q LOSS WILD-TYPE 388 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     50   22
  9Q LOSS WILD-TYPE  388  140
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON               50               388
  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        14         1         0
  9Q LOSS WILD-TYPE      88        1       32       157         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         68         46       47
                   vv
clus                STAGE IVA STAGE IVB
  9Q LOSS MUTATED           4         0
  9Q LOSS WILD-TYPE        23         2
D57V4, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 14                88
  STAGE IA                 0                 1
  STAGE II                 4                32
  STAGE IIA               14               157
  STAGE IIB                1                 9
  STAGE IIC                0                 3
  STAGE III                2                24
  STAGE IIIA               3                18
  STAGE IIIB              10                68
  STAGE IIIC               7                46
  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  42  12
  9Q LOSS WILD-TYPE  17  88 370  53
D57V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               3                17
  T2              17                88
  T3              42               370
  T4              12                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 LOSS MUTATED    36  22  16
  9Q LOSS WILD-TYPE 305 126  96
D57V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              36               305
  N1              22               126
  N2              16                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  9Q LOSS MUTATED    49  16   2   0   6
  9Q LOSS WILD-TYPE 397  58   8   2  57
D57V7, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               49               397
  M1               16                58
  M1A               2                 8
  M1B               0                 2
  MX                6                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    32  42
  9Q LOSS WILD-TYPE 251 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     32   42
  9Q LOSS WILD-TYPE  251  279
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              32               251
  MALE                42               279
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                     48                             2
  9Q LOSS WILD-TYPE                  330                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                      21                              1
  9Q LOSS WILD-TYPE                   125                             12
D57V9, multiclass
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        48               330
  COLON MUCINOUS ADENOCARCINOMA                2                57
  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
  9Q LOSS MUTATED     1  73
  9Q LOSS WILD-TYPE   8 522
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   73
  9Q LOSS WILD-TYPE    8  522
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 8
  YES              73               522
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    48   2   8   3
  9Q LOSS WILD-TYPE 388   3  28  26
D57V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              48               388
  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
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           6    39
  9Q LOSS WILD-TYPE                        50   253
D57V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      6                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(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    84  14
  10P LOSS WILD-TYPE 382  95
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                98                477 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                 95 
$`10P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       17.79        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 
        0.99        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         0.99        26.01        41.00         1.02 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 
        0.43        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        61.87        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         1.32         5.19        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        14.86 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        26.43 

$`10P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       23.38        42.28        44.91        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        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        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         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-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-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        14.93        17.03        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        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-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-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        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-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-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        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 
       48.20        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         8.02        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        14.99        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         7.92        15.12        17.85         4.50        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         1.28         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        43.07 
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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        2.79         5.98         5.59         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        6.64        14.76        67.00        17.95        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
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-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99         1.02        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-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        48.03        32.02        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-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        64.01        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.96        61.97        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.99        12.00         7.10        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.20               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             140.38 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            16.705             17.980 
[1] "0.2 - 129.3 (16.7)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.4"
D58V2, continuous
D58V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    66  33
  10P LOSS WILD-TYPE 372 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     66   33
  10P LOSS WILD-TYPE  372  129
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON                66                372
  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      86        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         64         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  10P LOSS MUTATED           6         1
  10P LOSS WILD-TYPE        21         1
D58V4, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  16                 86
  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                 64
  STAGE IIIC               11                 42
  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  85 345  54
D58V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                2                 18
  T2               20                 85
  T3               67                345
  T4               11                 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
  10P LOSS MUTATED    47  30  23
  10P LOSS WILD-TYPE 294 118  89
D58V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               47                294
  N1               30                118
  N2               23                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P LOSS MUTATED    70  16   2   1  10
  10P LOSS WILD-TYPE 376  58   8   1  53
D58V7, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                70                376
  M1                16                 58
  M1A                2                  8
  M1B                1                  1
  MX                10                 53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46  54
  10P LOSS WILD-TYPE 237 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46   54
  10P LOSS WILD-TYPE  237  267
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               46                237
  MALE                 54                267
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                     60                             6
  10P LOSS WILD-TYPE                  318                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                      27                              6
  10P LOSS WILD-TYPE                   119                              7
D58V9, multiclass
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         60                318
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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"
D58V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     5  95
  10P LOSS WILD-TYPE   4 500
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   95
  10P LOSS WILD-TYPE    4  500
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 5                  4
  YES               95                500
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    75   0   6   5
  10P LOSS WILD-TYPE 361   5  30  24
D58V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               75                361
  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"
D58V12, 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                        47   236
D58V13, 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                 47
  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(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    91  15
  10Q LOSS WILD-TYPE 375  94
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               106                469 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 94 
$`10Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 
       37.02        17.79        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         0.99        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         0.99 
TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
       26.01        41.00         1.02         0.43        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         7.92         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-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 
        1.32         5.19        30.28        24.13        13.55        12.72 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 
       10.39        65.98        32.02        46.03        34.03         6.05 
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-A011 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X TCGA-CI-6624 TCGA-DC-6155 
       37.02        12.00        10.98        41.00         4.73        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
       36.00        13.05        10.06       129.27        24.13         0.49 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 
       17.00        16.34        16.31        16.41        11.97        14.86 
TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
        0.66         0.46        47.08        26.43 

$`10Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        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-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84        52.44         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
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-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-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         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-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        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-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         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-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        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-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         1.58         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.46         0.92        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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        48.20        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         8.02        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 
       14.99        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         4.50 
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         1.28         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 
       43.07        61.87        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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        10.52         2.79         5.98         5.59         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       26.99        17.29         6.64        14.76        67.00        17.95 
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 
        8.45        15.39        20.02        86.63        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         1.02         2.01        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-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99         1.02        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-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        48.03        32.02        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-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        51.98        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-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       12.95         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        1.02         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 
       55.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.26               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             140.38 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             17.39              17.95 
[1] "0.3 - 129.3 (17.4)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.4"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    71  37
  10Q LOSS WILD-TYPE 367 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     71   37
  10Q LOSS WILD-TYPE  367  125
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON                71                367
  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        26         1         1
  10Q LOSS WILD-TYPE      85        1       31       145         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         64         39       48
                    vv
clus                 STAGE IVA STAGE IVB
  10Q LOSS MUTATED           5         1
  10Q LOSS WILD-TYPE        22         1
D59V4, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 85
  STAGE IA                  0                  1
  STAGE II                  5                 31
  STAGE IIA                26                145
  STAGE IIB                 1                  9
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                6                 15
  STAGE IIIB               14                 64
  STAGE IIIC               14                 39
  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  74  11
  10Q LOSS WILD-TYPE  17  85 338  54
D59V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                3                 17
  T2               20                 85
  T3               74                338
  T4               11                 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
  10Q LOSS MUTATED    54  29  25
  10Q LOSS WILD-TYPE 287 119  87
D59V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               54                287
  N1               29                119
  N2               25                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10Q LOSS MUTATED    80  15   2   1  10
  10Q LOSS WILD-TYPE 366  59   8   1  53
D59V7, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                80                366
  M1                15                 59
  M1A                2                  8
  M1B                1                  1
  MX                10                 53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    50  59
  10Q LOSS WILD-TYPE 233 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     50   59
  10Q LOSS WILD-TYPE  233  262
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               50                233
  MALE                 59                262
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                     65                             6
  10Q LOSS WILD-TYPE                  313                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                      31                              6
  10Q LOSS WILD-TYPE                   115                              7
D59V9, multiclass
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         65                313
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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"
D59V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5 104
  10Q LOSS WILD-TYPE   4 491
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5  104
  10Q LOSS WILD-TYPE    4  491
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 5                  4
  YES              104                491
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    82   1   7   5
  10Q LOSS WILD-TYPE 354   4  29  24
D59V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               82                354
  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"
D59V12, 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    58
  10Q LOSS WILD-TYPE                        46   234
D59V13, 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                 46
  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(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    59  11
  11P LOSS WILD-TYPE 407  98
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                70                505 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                 98 
$`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         1.58         0.43        14.50         0.20         5.52 
TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5863 
        1.41         2.14         0.26        48.20         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 
       15.02        14.04        11.01        14.99        20.19         7.92 
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         4.11         1.32 
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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        34.65 
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-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         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-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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        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-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         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-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
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-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       33.07        36.03         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-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00        20.98        34.03        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        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-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-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
        0.95        15.75        21.44        17.82         5.19         6.87 
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 
        8.02        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         4.50        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         1.28         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 
       43.07        61.87        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        10.52         2.79         5.98         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       30.28        67.00        24.13        17.95        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       19.10        12.72        37.74        10.39         8.45        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 
        1.02         2.01        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-3742 
       19.99         7.99         0.99        29.98         1.02         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-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        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-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-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-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         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        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       10.98        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
        7.10        30.05        12.95        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         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-F5-6814 
       31.30        14.86         0.39         1.02         0.66         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 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             50.99             140.38 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             14.50              18.05 
[1] "0.2 - 51.0 (14.5)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  23
  11P LOSS WILD-TYPE 388 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   23
  11P LOSS WILD-TYPE  388  139
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON                50                388
  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      87        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         68         42       53
                    vv
clus                 STAGE IVA STAGE IVB
  11P LOSS MUTATED           5         1
  11P LOSS WILD-TYPE        22         1
D60V4, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  15                 87
  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                 68
  STAGE IIIC               11                 42
  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  91 366  53
D60V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 18
  T2               14                 91
  T3               46                366
  T4               12                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11P LOSS MUTATED    31  24  19
  11P LOSS WILD-TYPE 310 124  93
D60V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               31                310
  N1               24                124
  N2               19                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  11P LOSS MUTATED    50   8   4   1  10
  11P LOSS WILD-TYPE 396  66   6   1  53
D60V7, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                50                396
  M1                 8                 66
  M1A                4                  6
  M1B                1                  1
  MX                10                 53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    34  40
  11P LOSS WILD-TYPE 249 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     34   40
  11P LOSS WILD-TYPE  249  281
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               34                249
  MALE                 40                281
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                     43                             7
  11P LOSS WILD-TYPE                  335                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                      18                              4
  11P LOSS WILD-TYPE                   128                              9
D60V9, multiclass
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         43                335
  COLON MUCINOUS ADENOCARCINOMA                 7                 52
  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"
D60V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  72
  11P LOSS WILD-TYPE   7 523
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   72
  11P LOSS WILD-TYPE    7  523
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 2                  7
  YES               72                523
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    53   0   5   4
  11P LOSS WILD-TYPE 383   5  31  25
D60V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               53                383
  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"
D60V12, 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                        52   257
D60V13, 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                 52
  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(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    69  16
  11Q LOSS WILD-TYPE 397  93
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                85                490 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                 93 
$`11Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 
       37.02        15.52        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         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D 
        1.02         0.43        14.50         0.95         0.20         5.52 
TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5862 
        1.41         2.14         0.26         2.01        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-5537 
       15.02        15.02        14.04        11.01        11.01        14.99 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1D6 
       20.19         7.92        17.85        14.30       130.65        49.91 
TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC TCGA-AF-2691 
        7.50        36.72        36.00         4.11         1.32        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 
       13.55        19.10        14.50        15.39        10.39        32.02 
TCGA-AG-3581 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 
        7.07         2.01         6.05        32.98         1.02        13.94 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CL-4957 
       12.00        10.98         0.49         0.69        10.19        13.97 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 
       13.97         7.10        30.05         5.29        24.13        17.00 
TCGA-EI-6881 
       16.41 

$`11Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        16.04        34.65        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-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-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         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        36.03         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-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-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03         2.01        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         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         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        51.98         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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31        15.75        21.44        17.82         5.19         6.87 
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-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        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-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 
       22.03        22.98        16.01        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-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
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-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       11.51        20.42        17.75        18.25         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20        92.75        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 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         1.28         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        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        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        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       14.76        30.28        67.00        24.13        17.95        17.23 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        37.74        10.39         8.45        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 
       65.98        11.84        36.03        12.00         8.02         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        2.01        24.00         1.02        46.03        34.03        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-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        20.98         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-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-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        41.00        38.04         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.99        12.00        15.02        36.00        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        14.86         0.39         1.02 
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 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            130.65             140.38 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             14.50              18.28 
[1] "0.2 - 130.7 (14.5)" "0.1 - 140.4 (18.3)"
[1] "hr=" "1.4"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    60  27
  11Q LOSS WILD-TYPE 378 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     60   27
  11Q LOSS WILD-TYPE  378  135
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON                60                378
  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        18        0        2        21         0         0
  11Q LOSS WILD-TYPE      84        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         65         43       49
                    vv
clus                 STAGE IVA STAGE IVB
  11Q LOSS MUTATED           4         1
  11Q LOSS WILD-TYPE        23         1
D61V4, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  18                 84
  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                 65
  STAGE IIIC               10                 43
  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  15  60  12
  11Q LOSS WILD-TYPE  16  90 352  53
D61V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 16
  T2               15                 90
  T3               60                352
  T4               12                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11Q LOSS MUTATED    43  30  18
  11Q LOSS WILD-TYPE 298 118  94
D61V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               43                298
  N1               30                118
  N2               18                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  11Q LOSS MUTATED    61  12   3   1  11
  11Q LOSS WILD-TYPE 385  62   7   1  52
D61V7, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                61                385
  M1                12                 62
  M1A                3                  7
  M1B                1                  1
  MX                11                 52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    45  46
  11Q LOSS WILD-TYPE 238 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     45   46
  11Q LOSS WILD-TYPE  238  275
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               45                238
  MALE                 46                275
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                     52                             8
  11Q LOSS WILD-TYPE                  326                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                      21                              5
  11Q LOSS WILD-TYPE                   125                              8
D61V9, multiclass
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         52                326
  COLON MUCINOUS ADENOCARCINOMA                 8                 51
  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"
D61V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  88
  11Q LOSS WILD-TYPE   6 507
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   88
  11Q LOSS WILD-TYPE    6  507
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                  6
  YES               88                507
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    64   0   6   4
  11Q LOSS WILD-TYPE 372   5  30  25
D61V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               64                372
  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"
D61V12, 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                           4    48
  11Q LOSS WILD-TYPE                        52   244
D61V13, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                       4                 52
  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(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    49  17
  12P LOSS WILD-TYPE 417  92
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                66                509 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                 92 
$`12P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-6782 
       37.02        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         1.58         1.02         0.43 
TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
       65.00         2.14        48.20         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        61.87 
TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-3913 
       36.72        36.00         5.19        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         7.10        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        14.86         0.66 

$`12P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        16.04        14.53        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-A6-5666 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 
       52.44         5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       29.00        12.99         0.99        14.01        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-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-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         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        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-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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72         0.10         0.76         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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         8.02        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        14.99        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 
        7.92        15.12        17.85         4.50        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         1.28 
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        43.07        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         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       17.29         6.64        14.76        67.00        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       17.23        13.55        19.10        12.72        37.74         8.45 
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         1.02         2.01 
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-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-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-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-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-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        1.45         0.69         0.72         4.60         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        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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-6510 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         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-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.43               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             140.38 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            16.705             17.950 
[1] "0.4 - 70.0 (16.7)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.5"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    46  23
  12P LOSS WILD-TYPE 392 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     46   23
  12P LOSS WILD-TYPE  392  139
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON                46                392
  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      92        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         68         42       52
                    vv
clus                 STAGE IVA STAGE IVB
  12P LOSS MUTATED           5         0
  12P LOSS WILD-TYPE        22         2
D62V4, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  10                 92
  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                 68
  STAGE IIIC               11                 42
  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  96 358  61
D62V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 17
  T2                9                 96
  T3               54                358
  T4                4                 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
  12P LOSS MUTATED    30  23  17
  12P LOSS WILD-TYPE 311 125  95
D62V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               30                311
  N1               23                125
  N2               17                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  12P LOSS MUTATED    45  12   1   0  10
  12P LOSS WILD-TYPE 401  62   9   2  53
D62V7, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                45                401
  M1                12                 62
  M1A                1                  9
  M1B                0                  2
  MX                10                 53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    34  36
  12P LOSS WILD-TYPE 249 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     34   36
  12P LOSS WILD-TYPE  249  285
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               34                249
  MALE                 36                285
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                     45                             1
  12P LOSS WILD-TYPE                  333                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                      23                              0
  12P LOSS WILD-TYPE                   123                             13
D62V9, multiclass
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         45                333
  COLON MUCINOUS ADENOCARCINOMA                 1                 58
  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"
D62V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  67
  12P LOSS WILD-TYPE   6 528
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   67
  12P LOSS WILD-TYPE    6  528
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                  6
  YES               67                528
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    54   0   4   2
  12P LOSS WILD-TYPE 382   5  32  27
D62V11, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               54                382
  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"
D62V12, 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                        50   251
D62V13, 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                 50
  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(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    52  15
  12Q LOSS WILD-TYPE 414  94
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                67                508 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 94 
$`12Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       37.02        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         1.58         1.02         0.43 
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        48.20         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        61.87        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         7.10 
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        14.86 
TCGA-F5-6812 
        0.66 

$`12Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        16.04        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        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-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        14.01        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        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-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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        27.09        16.31         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        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         8.02 
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        14.99        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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        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         1.28         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 
       43.07        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 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       14.76        67.00        24.13        17.95        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       19.10        12.72        37.74        10.39         8.45        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         1.02         2.01        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-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-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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         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-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
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-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24       129.27        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.97         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         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 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.20               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             61.87             140.38 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            16.310             17.965 
[1] "0.2 - 61.9 (16.3)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "1.4"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    48  20
  12Q LOSS WILD-TYPE 390 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     48   20
  12Q LOSS WILD-TYPE  390  142
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON                48                390
  RECTUM               20                142
[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         0
  12Q LOSS WILD-TYPE      91        1       35       157         9         3
                    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         69         42       52
                    vv
clus                 STAGE IVA STAGE IVB
  12Q LOSS MUTATED           5         0
  12Q LOSS WILD-TYPE        22         2
D63V4, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  11                 91
  STAGE IA                  0                  1
  STAGE II                  1                 35
  STAGE IIA                14                157
  STAGE IIB                 1                  9
  STAGE IIC                 0                  3
  STAGE III                 1                 25
  STAGE IIIA                4                 17
  STAGE IIIB                9                 69
  STAGE IIIC               11                 42
  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  51   4
  12Q LOSS WILD-TYPE  17  94 361  61
D63V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 17
  T2               11                 94
  T3               51                361
  T4                4                 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
  12Q LOSS MUTATED    29  23  17
  12Q LOSS WILD-TYPE 312 125  95
D63V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               29                312
  N1               23                125
  N2               17                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  12Q LOSS MUTATED    43  13   1   0   9
  12Q LOSS WILD-TYPE 403  61   9   2  54
D63V7, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                43                403
  M1                13                 61
  M1A                1                  9
  M1B                0                  2
  MX                 9                 54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    32  37
  12Q LOSS WILD-TYPE 251 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     32   37
  12Q LOSS WILD-TYPE  251  284
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               32                251
  MALE                 37                284
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                     46                             2
  12Q LOSS WILD-TYPE                  332                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                      20                              0
  12Q LOSS WILD-TYPE                   126                             13
D63V9, multiclass
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         46                332
  COLON MUCINOUS ADENOCARCINOMA                 2                 57
  RECTAL ADENOCARCINOMA                        20                126
  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
  12Q LOSS MUTATED     2  67
  12Q LOSS WILD-TYPE   7 528
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   67
  12Q LOSS WILD-TYPE    7  528
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 2                  7
  YES               67                528
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    51   0   4   3
  12Q LOSS WILD-TYPE 385   5  32  26
D63V11, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               51                385
  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"
D63V12, 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    44
  12Q LOSS WILD-TYPE                        52   248
D63V13, 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                 52
  WHITE                                          44                248
[1] 4 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 = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   4
  13Q LOSS WILD-TYPE 453 105
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                558 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                105 
$`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         0.99         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         6.64         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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 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        52.44         9.63         5.03         1.02         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-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-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        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         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        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-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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         1.58         1.02         0.10         0.76         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         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         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        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        48.20        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         8.02        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 
       14.99        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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        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         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       14.76        30.28        67.00        24.13        17.95        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         8.45        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         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        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-A011 
        0.99        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        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         4.60         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        60.03         7.99 
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         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-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        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         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 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.20               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             140.38 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.98              17.90 
[1] "0.2 - 126.4 (11.0)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.4"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    12   8
  13Q LOSS WILD-TYPE 426 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    8
  13Q LOSS WILD-TYPE  426  154
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON                12                426
  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      99        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         77         49       58
                    vv
clus                 STAGE IVA STAGE IVB
  13Q LOSS MUTATED           2         0
  13Q LOSS WILD-TYPE        25         2
D64V4, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                 99
  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                 77
  STAGE IIIC                4                 49
  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  19 103 398  62
D64V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                1                 19
  T2                2                103
  T3               14                398
  T4                3                 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
  13Q LOSS MUTATED     9   3   8
  13Q LOSS WILD-TYPE 332 145 104
D64V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                9                332
  N1                3                145
  N2                8                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  13Q LOSS MUTATED    11   3   2   0   3
  13Q LOSS WILD-TYPE 435  71   8   2  60
D64V7, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                11                435
  M1                 3                 71
  M1A                2                  8
  M1B                0                  2
  MX                 3                 60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  11
  13Q LOSS WILD-TYPE 274 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE  274  310
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                274
  MALE                 11                310
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                      8                             3
  13Q LOSS WILD-TYPE                  370                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                       6                              2
  13Q LOSS WILD-TYPE                   140                             11
D64V9, multiclass
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          8                370
  COLON MUCINOUS ADENOCARCINOMA                 3                 56
  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"
D64V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  20
  13Q LOSS WILD-TYPE   9 575
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   20
  13Q LOSS WILD-TYPE    9  575
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  9
  YES               20                575
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    16   0   1   1
  13Q LOSS WILD-TYPE 420   5  35  28
D64V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               16                420
  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"
D64V12, 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                        55   285
D64V13, 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                 55
  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(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   156  34
  14Q LOSS WILD-TYPE 310  75
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               190                385 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                34                 75 
$`14Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       37.02        42.28        35.11        15.52        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 
       14.53        32.45        32.91        30.44        23.61        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       20.28        61.84         5.03         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 
       24.03        19.07        34.03        13.02        23.01        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       19.99         2.01        14.01        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 
       19.00        85.05         0.99        25.02        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3939 
       17.03        31.07        17.03        24.03        18.05        12.99 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       24.00         7.96        17.03        27.02        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       21.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         1.58         1.02         0.10 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
        0.43        14.50         0.95        15.75         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
       75.25         1.41         5.65        22.36        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 
        1.94         3.06         2.14         0.07         0.26        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        2.01         8.02         8.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       13.02        15.02        11.08        10.06        14.99        12.26 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 
       13.51        18.25         1.32        15.12        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A288 TCGA-DM-A28E 
       11.38        38.20        13.32       140.38        14.04       119.93 
TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 
       13.38        29.59        33.67         1.28         0.53        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V 
        8.35        82.39        36.72        91.79         4.11        10.52 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 
        5.59         5.19         5.49        30.28        17.95        17.23 
TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 
       13.55        37.74        10.39        65.98        11.84         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 
       46.03        34.03        50.04         6.05         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 
        1.02        17.03        35.01         1.02        48.03        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 
       14.04        17.03         6.02        25.97        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04         0.49        10.19         6.05         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        13.97         7.99        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        36.00         7.10        13.05        10.06       129.27 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       51.48        20.55        17.00        16.34        16.31        16.41 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        11.97        31.30         0.39         1.02         0.66 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        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 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       17.79        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 
       16.04        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         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-3532 TCGA-AA-3534 
       37.05        36.03         8.05        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       24.00        17.95        29.95        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.05         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       15.95        38.99        14.93         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 
        2.01        20.98         2.01        13.05        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72         0.76         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31         0.20        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
       50.37        58.39        32.94         5.13        83.80        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-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74         3.19         2.24         3.25         3.29         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-6751 
       15.62        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.03        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75         7.92        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F 
        7.76       139.17         6.12        26.47        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 
       16.24        35.41        19.43       107.67        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        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-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV 
       52.80        10.98         2.79         5.98         1.32        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 
       17.29         6.64        14.76        67.00        24.13        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        86.63        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 
        7.07         2.01        24.00         1.02         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
        0.99        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
        1.02        32.98         0.99        19.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       14.01        32.02        19.99        28.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        13.94        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 
        0.72         4.60         1.81         6.97        60.03        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        30.05        12.95         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-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       37.51        14.86         0.69         0.53         1.12         0.46 
TCGA-G5-6572 
       47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            140.38             139.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            16.375             19.040 
[1] "0.1 - 140.4 (16.4)" "0.1 - 139.2 (19.0)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   133  66
  14Q LOSS WILD-TYPE 305  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    133   66
  14Q LOSS WILD-TYPE  305   96
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON               133                305
  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      72        1       28       113         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED          10          9         27         15       26
  14Q LOSS WILD-TYPE        16         12         51         38       35
                    vv
clus                 STAGE IVA STAGE IVB
  14Q LOSS MUTATED          12         0
  14Q LOSS WILD-TYPE        15         2
D65V4, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  30                 72
  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               27                 51
  STAGE IIIC               15                 38
  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  18
  14Q LOSS WILD-TYPE  11  74 269  47
D65V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                9                 11
  T2               31                 74
  T3              143                269
  T4               18                 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   104  62  35
  14Q LOSS WILD-TYPE 237  86  77
D65V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              104                237
  N1               62                 86
  N2               35                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  14Q LOSS MUTATED   142  35   3   0  19
  14Q LOSS WILD-TYPE 304  39   7   2  44
D65V7, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               142                304
  M1                35                 39
  M1A                3                  7
  M1B                0                  2
  MX                19                 44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    91 110
  14Q LOSS WILD-TYPE 192 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     91  110
  14Q LOSS WILD-TYPE  192  211
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               91                192
  MALE                110                211
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                    128                             4
  14Q LOSS WILD-TYPE                  250                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                      64                              1
  14Q LOSS WILD-TYPE                    82                             12
D65V9, multiclass
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        128                250
  COLON MUCINOUS ADENOCARCINOMA                 4                 55
  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"
D65V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     3 198
  14Q LOSS WILD-TYPE   6 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  198
  14Q LOSS WILD-TYPE    6  397
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 3                  6
  YES              198                397
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   140   2  12  10
  14Q LOSS WILD-TYPE 296   3  24  19
D65V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              140                296
  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"
D65V12, 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                          19    96
  14Q LOSS WILD-TYPE                        37   196
D65V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  8
  BLACK OR AFRICAN AMERICAN                      19                 37
  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(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   173  38
  15Q LOSS WILD-TYPE 293  71
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               211                364 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                38                 71 
$`15Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 
       37.02        43.76        43.43        17.79        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       15.52        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 
       29.16        22.52        25.08        20.61        21.76        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         1.02         1.02         6.97         9.07 
TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       37.05        29.00        12.99        33.99        21.01        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       23.01        19.99        19.99         2.01        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       19.00        36.00        85.05        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.03        29.98        12.99         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F 
       13.05        34.06        24.00        27.02        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       42.02        17.03        14.99        15.02        15.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         1.58         1.02 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D 
        0.10        14.50        16.31         0.95        15.75         5.52 
TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 
        6.87        83.80        65.00        62.79        61.41        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        5.23         3.19         2.14         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       48.20         2.01         8.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       20.19         1.32        15.12        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.13         9.04        13.41        11.38       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28M 
       13.32        12.59       140.38       131.51         6.12        95.18 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       13.38        35.87         1.55        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        0.53        35.41         8.35        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       36.72        36.00        91.79        46.75        10.98        10.52 
TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
        1.32        30.28        24.13        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       14.50        10.39        65.98        32.02         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
       24.00        46.03        34.03         6.05        19.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
        0.99        19.99        17.03        35.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        14.04        17.03        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       37.02         1.02        12.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
       38.04         0.49         0.69        10.19         6.05         9.37 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
        7.99        10.98        12.99        13.97        36.00        13.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 
       41.36        57.24        24.13         0.49         2.40        15.85 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 
       31.30        14.86         1.02         0.66         0.69        18.28 
TCGA-G5-6641 
       26.43 

$`15Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
        5.06         5.26        46.65        23.38        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        16.04        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 
       52.44         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-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       29.00        26.01         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        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-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 
       17.98        15.95        14.93        33.07        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-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-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       16.08        26.01        25.02        19.07         7.96        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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        4.01        27.02         0.99        21.99        34.98         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        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-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-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72         0.76         0.20         0.43         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
       27.09         0.20        21.44        17.82         5.19        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-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
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-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-4750 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        26.04         8.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
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-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       12.95        13.05        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.50        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       24.43        38.20        49.91         7.50        44.32       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-F4-6461 
       35.97        60.79       117.07        98.24         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 
       13.64        13.45         6.18        16.31        29.59        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        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80         4.11         2.79         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       17.95        17.23        19.10        12.72        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        8.02         7.07         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98         0.99         1.02        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02        36.03         1.02         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
        6.02        15.95        36.03         9.07        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       64.01        10.98        51.98        49.97        61.97         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.72         4.60         1.81         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       13.97        60.03        11.01        15.02        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 
       17.00        18.28        17.69        16.34         8.61        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        8.45         9.96        37.51         0.39         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        55.76        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.10               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            140.38             139.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            17.030             17.965 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (18.0)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   149  70
  15Q LOSS WILD-TYPE 289  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    149   70
  15Q LOSS WILD-TYPE  289   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON               149                289
  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        32        0        7        57         3         2
  15Q LOSS WILD-TYPE      70        1       29       114         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           7         11         29         25       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
D66V4, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  32                 70
  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               29                 49
  STAGE IIIC               25                 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  31 160  22
  15Q LOSS WILD-TYPE  11  74 252  43
D66V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                 11
  T2               31                 74
  T3              160                252
  T4               22                 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   108  65  49
  15Q LOSS WILD-TYPE 233  83  63
D66V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              108                233
  N1               65                 83
  N2               49                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  15Q LOSS MUTATED   154  36   6   1  21
  15Q LOSS WILD-TYPE 292  38   4   1  42
D66V7, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               154                292
  M1                36                 38
  M1A                6                  4
  M1B                1                  1
  MX                21                 42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    99 123
  15Q LOSS WILD-TYPE 184 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     99  123
  15Q LOSS WILD-TYPE  184  198
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               99                184
  MALE                123                198
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                    137                            11
  15Q LOSS WILD-TYPE                  241                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                      64                              5
  15Q LOSS WILD-TYPE                    82                              8
D66V9, multiclass
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        137                241
  COLON MUCINOUS ADENOCARCINOMA                11                 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"
D66V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7 215
  15Q LOSS WILD-TYPE   2 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7  215
  15Q LOSS WILD-TYPE    2  380
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                  2
  YES              215                380
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   158   2  15   9
  15Q LOSS WILD-TYPE 278   3  21  20
D66V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              158                278
  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"
D66V12, 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                          15   115
  15Q LOSS WILD-TYPE                        41   177
D66V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      15                 41
  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(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    28   9
  16P LOSS WILD-TYPE 438 100
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                538 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                100 
$`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         0.43         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         5.52         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         4.11        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         1.02         0.53 
TCGA-G5-6233 
       18.28 

$`16P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       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-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
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-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         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         0.99        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-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-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20         0.92        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         6.87        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        48.20        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         8.02 
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        14.99        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 
        7.92        15.12        17.85         4.50        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         1.28         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 
       43.07        61.87        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        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        67.00        24.13        17.95        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         8.45        15.39        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-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        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-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-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-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         4.60         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        60.03         7.99 
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         7.10        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 
       14.86         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 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.20               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             61.84             140.38 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            14.500             18.015 
[1] "0.2 - 61.8 (14.5)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "1.8"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    30  10
  16P LOSS WILD-TYPE 408 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     30   10
  16P LOSS WILD-TYPE  408  152
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON                30                408
  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      99        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         72         47       58
                    vv
clus                 STAGE IVA STAGE IVB
  16P LOSS MUTATED           4         0
  16P LOSS WILD-TYPE        23         2
D67V4, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   3                 99
  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                 72
  STAGE IIIC                6                 47
  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  20 101 381  60
D67V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                 20
  T2                4                101
  T3               31                381
  T4                5                 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
  16P LOSS MUTATED    21   8  11
  16P LOSS WILD-TYPE 320 140 101
D67V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               21                320
  N1                8                140
  N2               11                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  16P LOSS MUTATED    27   5   2   0   5
  16P LOSS WILD-TYPE 419  69   8   2  58
D67V7, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                27                419
  M1                 5                 69
  M1A                2                  8
  M1B                0                  2
  MX                 5                 58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    21  19
  16P LOSS WILD-TYPE 262 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     21   19
  16P LOSS WILD-TYPE  262  302
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               21                262
  MALE                 19                302
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                     24                             6
  16P LOSS WILD-TYPE                  354                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                       8                              1
  16P LOSS WILD-TYPE                   138                             12
D67V9, multiclass
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         24                354
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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"
D67V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  40
  16P LOSS WILD-TYPE   9 555
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   40
  16P LOSS WILD-TYPE    9  555
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  9
  YES               40                555
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    29   1   0   1
  16P LOSS WILD-TYPE 407   4  36  28
D67V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               29                407
  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"
D67V12, 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                        48   271
D67V13, 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                 48
  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(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    32   7
  16Q LOSS WILD-TYPE 434 102
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                39                536 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                102 
$`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         0.43        16.31 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 TCGA-CM-5863 
        0.20         5.52         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 
        4.11        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 
        1.02         0.53        18.28 

$`16Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
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-A6-6142 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-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        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        17.03         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         0.99        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         1.58         1.02         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         6.87        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        48.20        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 
        8.02        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        14.99 
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         7.92        15.12        17.85         4.50        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         1.28         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        43.07        61.87        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        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       26.99        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        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         8.45        15.39        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-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         0.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-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-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-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
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        60.03         7.99        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-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        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-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        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             41.00             140.38 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             13.05              18.05 
[1] "0.2 - 41.0 (13.1)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    28  14
  16Q LOSS WILD-TYPE 410 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     28   14
  16Q LOSS WILD-TYPE  410  148
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON                28                410
  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      96        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         72         46       57
                    vv
clus                 STAGE IVA STAGE IVB
  16Q LOSS MUTATED           3         0
  16Q LOSS WILD-TYPE        24         2
D68V4, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   6                 96
  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                 72
  STAGE IIIC                7                 46
  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  98 382  60
D68V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                 20
  T2                7                 98
  T3               30                382
  T4                5                 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
  16Q LOSS MUTATED    23   7  12
  16Q LOSS WILD-TYPE 318 141 100
D68V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               23                318
  N1                7                141
  N2               12                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16Q LOSS MUTATED    29   4   2   0   6
  16Q LOSS WILD-TYPE 417  70   8   2  57
D68V7, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                29                417
  M1                 4                 70
  M1A                2                  8
  M1B                0                  2
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  21
  16Q LOSS WILD-TYPE 262 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   21
  16Q LOSS WILD-TYPE  262  300
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                262
  MALE                 21                300
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                     23                             5
  16Q LOSS WILD-TYPE                  355                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                      12                              1
  16Q LOSS WILD-TYPE                   134                             12
D68V9, multiclass
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         23                355
  COLON MUCINOUS ADENOCARCINOMA                 5                 54
  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"
D68V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  41
  16Q LOSS WILD-TYPE   8 554
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   41
  16Q LOSS WILD-TYPE    8  554
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  8
  YES               41                554
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    30   1   1   1
  16Q LOSS WILD-TYPE 406   4  35  28
D68V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               30                406
  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"
D68V12, 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                        48   273
D68V13, 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                 48
  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(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   252  66
  17P LOSS WILD-TYPE 214  43
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               318                257 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                66                 43 
$`17P LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       37.02        43.76        43.43        17.79        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 
       15.52        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         1.02         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 
        0.99        25.02        38.99        36.95        37.02         0.99 
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        17.03        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         0.99 
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         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         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         5.52        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        48.20        21.99         2.01         8.02 
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        14.99        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 
        7.92        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         1.28         8.35        23.51        61.87        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        10.52         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        37.74        14.50        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        12.00        32.02         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3726 
       24.00        34.03         2.01        50.04         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 
        0.99         1.02        32.98         0.99         1.02        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-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
       64.01        51.98         1.94        41.00         0.49         0.69 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        0.72        10.19         6.05         6.05         6.97        13.97 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 
        7.99        11.01        13.97         7.10        30.05        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-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       51.48         0.49         2.40        20.91        17.00        18.28 
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-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.39         0.69         0.53         0.76         0.46        55.76 

$`17P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2681 
        5.06         5.26        46.65        23.38        44.91        45.60 
TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       13.94        16.04        36.53        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 
       22.09        22.06         8.38        25.08        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
        9.63         3.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       13.02         1.02         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       29.00        26.01         0.99        17.95        29.95        20.98 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        15.02        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 
        1.02        17.98        15.95        14.93        17.03        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       24.00         2.01        21.99        13.05        34.06        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I 
       18.05         4.01         0.99        34.98        15.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
        0.07        56.55         0.72         0.76         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19         6.87        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         4.50        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        43.07        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-A5Z2 
       26.17        47.15        52.80         4.11         2.79        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 
       67.00        24.13        10.39         8.45        10.39        36.03 
TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3600 
        8.02         2.01         1.02        46.03        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        19.99        29.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4022 
       36.95        17.03        13.02        14.01         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       20.98        36.03         9.07        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6623 
       61.97        38.04         1.45         4.60         1.81         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        4.73        60.03        10.98        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1H8 TCGA-EI-6506 
       15.02        36.00        12.95        13.05        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 
       19.96        15.85         8.61        13.64        17.46         1.02 
TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.66         1.12        18.28        47.08        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            140.38             135.65 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             17.03              19.04 
[1] "0.1 - 140.4 (17.0)" "0.1 - 135.7 (19.0)"
[1] "hr=" "1.3"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   228 102
  17P LOSS WILD-TYPE 210  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    228  102
  17P LOSS WILD-TYPE  210   60
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON               228                210
  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        45        0       18        84         3         2
  17P LOSS WILD-TYPE      57        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         33         16       18
                    vv
clus                 STAGE IVA STAGE IVB
  17P LOSS MUTATED          18         2
  17P LOSS WILD-TYPE         9         0
D69V4, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  45                 57
  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                 33
  STAGE IIIC               37                 16
  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  53 233  39
  17P LOSS WILD-TYPE  11  52 179  26
D69V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                9                 11
  T2               53                 52
  T3              233                179
  T4               39                 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
  17P LOSS MUTATED   166  93  73
  17P LOSS WILD-TYPE 175  55  39
D69V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              166                175
  N1               93                 55
  N2               73                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  17P LOSS MUTATED   236  53   6   2  33
  17P LOSS WILD-TYPE 210  21   4   0  30
D69V7, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               236                210
  M1                53                 21
  M1A                6                  4
  M1B                2                  0
  MX                33                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   149 185
  17P LOSS WILD-TYPE 134 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    149  185
  17P LOSS WILD-TYPE  134  136
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              149                134
  MALE                185                136
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                    212                            15
  17P LOSS WILD-TYPE                  166                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                      95                              6
  17P LOSS WILD-TYPE                    51                              7
D69V9, multiclass
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        212                166
  COLON MUCINOUS ADENOCARCINOMA                15                 44
  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"
D69V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7 327
  17P LOSS WILD-TYPE   2 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7  327
  17P LOSS WILD-TYPE    2  268
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 7                  2
  YES              327                268
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   234   3  25  11
  17P LOSS WILD-TYPE 202   2  11  18
D69V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              234                202
  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"
D69V12, 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                          29   165
  17P LOSS WILD-TYPE                        27   127
D69V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      29                 27
  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(70) Variable = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    69  21
  17Q LOSS WILD-TYPE 397  88
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                90                485 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                 88 
$`17Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5666 TCGA-A6-6649 
       37.02        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         0.99        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 
        0.99        32.02        33.04        37.02         2.96        39.98 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D 
        1.58         1.02         0.20        14.50         0.20         5.52 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 
       12.10         3.29         0.26        48.20        27.02        13.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6924 
        5.03        15.02        14.99         7.92        12.49        14.30 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6704 
       11.38        38.20        12.59       140.38        13.38         1.55 
TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6314 TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A6GC 
        1.28         8.35        35.93        10.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
        5.19        26.99        17.29        14.50        15.39        65.98 
TCGA-AG-3582 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H 
        1.02         1.02        32.02        28.04        13.94        25.97 
TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A02X TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 
       12.00        51.98        41.00        10.19        13.97         7.10 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6512 
       10.06         5.29        24.13         0.49         2.40        17.69 
TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 
       16.41        11.51        14.86         0.53         0.76        55.76 

$`17Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
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        15.52 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1.02         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 
        1.02        13.02        38.99         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01         0.99        14.01        33.99        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-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        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-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 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        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-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 
       13.05        34.06        25.02        24.00        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02        15.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        39.06        51.98         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-6963 
       21.37         4.21        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.43         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
        0.95        15.75        21.44        17.82         5.19         6.87 
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-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-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-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        26.04         8.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        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-D5-5538 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         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        33.67         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 
       43.07        61.87        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-G4-6323 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-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11        10.52         2.79         5.98 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        5.49         6.64        14.76        30.28        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        10.39         8.45        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        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-3898 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        48.03        19.99        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-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-A020 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        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-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         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-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        13.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.31         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30         0.39         1.02         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.46        18.28        47.08        26.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            140.38             139.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             14.50              18.05 
[1] "0.2 - 140.4 (14.5)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.6"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    64  28
  17Q LOSS WILD-TYPE 374 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     64   28
  17Q LOSS WILD-TYPE  374  134
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON                64                374
  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        10        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           3          5         14         13       11
  17Q LOSS WILD-TYPE        23         16         64         40       50
                    vv
clus                 STAGE IVA STAGE IVB
  17Q LOSS MUTATED           6         1
  17Q LOSS WILD-TYPE        21         1
D70V4, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  10                 92
  STAGE IA                  0                  1
  STAGE II                  6                 30
  STAGE IIA                18                153
  STAGE IIB                 1                  9
  STAGE IIC                 2                  1
  STAGE III                 3                 23
  STAGE IIIA                5                 16
  STAGE IIIB               14                 64
  STAGE IIIC               13                 40
  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  14  64  15
  17Q LOSS WILD-TYPE  20  91 348  50
D70V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                 20
  T2               14                 91
  T3               64                348
  T4               15                 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
  17Q LOSS MUTATED    40  31  22
  17Q LOSS WILD-TYPE 301 117  90
D70V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               40                301
  N1               31                117
  N2               22                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  17Q LOSS MUTATED    59  13   3   1  14
  17Q LOSS WILD-TYPE 387  61   7   1  49
D70V7, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                59                387
  M1                13                 61
  M1A                3                  7
  M1B                1                  1
  MX                14                 49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    40  53
  17Q LOSS WILD-TYPE 243 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     40   53
  17Q LOSS WILD-TYPE  243  268
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               40                243
  MALE                 53                268
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                     55                             9
  17Q LOSS WILD-TYPE                  323                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                      26                              2
  17Q LOSS WILD-TYPE                   120                             11
D70V9, multiclass
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         55                323
  COLON MUCINOUS ADENOCARCINOMA                 9                 50
  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"
D70V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  91
  17Q LOSS WILD-TYPE   7 504
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   91
  17Q LOSS WILD-TYPE    7  504
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  7
  YES               91                504
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    66   1   7   6
  17Q LOSS WILD-TYPE 370   4  29  23
D70V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               66                370
  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"
D70V12, 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                          10    44
  17Q LOSS WILD-TYPE                        46   248
D70V13, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      10                 46
  WHITE                                          44                248
[1] 4 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 = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   292  65
  18P LOSS WILD-TYPE 174  44
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               357                218 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                65                 44 
$`18P LOSS MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
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        15.52 
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-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       29.16        27.09        24.13        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        37.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01        12.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.05         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 
       15.02        37.05        19.00        36.00        85.05        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       33.07         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       27.02        29.98        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-3975 
       34.03        21.99        16.08        50.99        13.05        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-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       17.03        27.02        42.02        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       15.02        32.02        31.00         1.02        33.04        26.01 
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         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.43        14.50         0.95        15.75         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        6.87        75.25         5.65         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
       65.00        62.79        12.10        29.56         5.23         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       48.20        21.99         2.01         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        13.51        11.51        20.19        18.25         1.32 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
       17.85        17.13        12.49         7.53        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17        14.04        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 
       95.18         8.61        13.38        11.11        13.45         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         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       35.41        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       55.04        45.11        35.93        36.72        36.00        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       47.15         4.11        10.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       26.99        17.29         6.64        30.28        24.13        17.95 
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-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       14.50        15.39        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       46.03        34.03        50.04         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        7.99        29.98         1.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        36.95        17.03        35.01         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-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       10.98        51.98         1.94        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60        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        60.03         7.99 
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         7.10        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-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 
       51.48         0.49         2.40        20.55        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       10.78        13.64        11.97        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39         1.02         0.66         0.69         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       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        23.38        16.04        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-3534 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
        8.05        29.00         0.99        21.01        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       20.98         6.97        54.02         0.92        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.98         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 
       35.05         0.99         1.02        17.98        15.95        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       32.05        53.00        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       24.00         2.01         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-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
        0.99        17.03        34.98         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07         1.02        35.01        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
       21.37        56.55         0.72         0.76         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
       27.09        16.31         0.20        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39         1.41        32.94        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
      100.01        11.74         3.19         3.06         3.25         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-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        27.02        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 
       12.95        13.05        11.08        19.59        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        7.92        15.12         4.50        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       10.13         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 
      119.70        92.75         7.50       135.65         7.76         6.12 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       81.37        60.79        98.24        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        43.07        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       51.75        39.42        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 
        5.98         5.59        14.76        67.00        19.10         8.45 
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               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.38             135.65 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             17.13              18.05 
[1] "0.1 - 140.4 (17.1)" "0.1 - 135.7 (18.1)"
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   243 126
  18P LOSS WILD-TYPE 195  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    243  126
  18P LOSS WILD-TYPE  195   36
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON               243                195
  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        56        0       16        97         4         3
  18P LOSS WILD-TYPE      46        1       20        74         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          11         14         53         37       49
  18P LOSS WILD-TYPE        15          7         25         16       12
                    vv
clus                 STAGE IVA STAGE IVB
  18P LOSS MUTATED          23         1
  18P LOSS WILD-TYPE         4         1
D71V4, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  56                 46
  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               53                 25
  STAGE IIIC               37                 16
  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  61 259  40
  18P LOSS WILD-TYPE   8  44 153  25
D71V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               12                  8
  T2               61                 44
  T3              259                153
  T4               40                 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   190 103  77
  18P LOSS WILD-TYPE 151  45  35
D71V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              190                151
  N1              103                 45
  N2               77                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  18P LOSS MUTATED   260  62   9   1  36
  18P LOSS WILD-TYPE 186  12   1   1  27
D71V7, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               260                186
  M1                62                 12
  M1A                9                  1
  M1B                1                  1
  MX                36                 27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   171 201
  18P LOSS WILD-TYPE 112 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    171  201
  18P LOSS WILD-TYPE  112  120
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              171                112
  MALE                201                120
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                    230                            12
  18P LOSS WILD-TYPE                  148                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                     119                              7
  18P LOSS WILD-TYPE                    27                              6
D71V9, multiclass
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        230                148
  COLON MUCINOUS ADENOCARCINOMA                12                 47
  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"
D71V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     8 364
  18P LOSS WILD-TYPE   1 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8  364
  18P LOSS WILD-TYPE    1  231
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 8                  1
  YES              364                231
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   265   2  29  14
  18P LOSS WILD-TYPE 171   3   7  15
D71V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              265                171
  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"
D71V12, 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                          35   184
  18P LOSS WILD-TYPE                        21   108
D71V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      35                 21
  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(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   312  73
  18Q LOSS WILD-TYPE 154  36
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               385                190 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                 36 
$`18Q LOSS MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
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        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 
       22.09        32.71        29.16        27.09        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        6.97        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       14.01        33.99        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03         0.99        33.07         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       12.99        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
       27.02         7.96        19.00        34.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
       39.98         2.01         5.03        41.00        40.96         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         1.58         1.02         0.10         0.20         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.46        14.50        16.31        15.75         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        6.87        75.25         5.65         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        61.41        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-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        1.35       102.44        48.20        21.99         2.01         8.02 
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-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       21.99        13.02        15.02        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       13.51        11.51        20.19        18.25         1.32        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
       17.13        12.49        15.58         7.53        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        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-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       131.51       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      119.93       117.07        95.18         8.61        13.38        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       13.45         1.55        16.31        29.59        16.24         1.28 
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-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       61.87        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.72        36.00        91.79        46.75        47.15         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        10.52         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       26.99        17.29         6.64        30.28        24.13        17.95 
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-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-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00        46.03        34.03         2.01        50.04 
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-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01         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-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.69         0.72         4.60        10.19         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        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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         7.10        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-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.41        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       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        23.38        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-3534 TCGA-AA-3543 
        1.02        13.02         1.02         8.05        29.00         0.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 
       21.01        17.95        29.95        20.98         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
        0.92        47.05        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-3821 
       19.04         0.99         0.99        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 
       17.98        15.95        36.03        32.05        53.00        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        17.03         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 
        0.07        21.37        56.55         0.72         0.76         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
       27.09         0.95         0.20        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         1.41        32.94        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-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56        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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       22.98        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 
       14.99        12.99        14.04        12.95        13.05        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       17.75         7.92        15.12         4.50        16.14        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       10.13         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      119.70       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        13.64         6.18        35.87        33.67        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      107.67        74.56        43.07        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AF-6672 
        2.79         5.59        14.76        67.00         8.45        10.39 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 
        8.02         1.02        12.03         6.05        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N 
       13.02        14.01        20.98        36.03        49.97        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 
        1.45         1.81         5.29        32.61        19.96         8.61 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       17.46         9.96         0.53         1.12 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            140.38             135.65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             17.13              18.05 
[1] "0.1 - 140.4 (17.1)" "0.1 - 135.7 (18.1)"
[1] "hr=" "1"  
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   262 136
  18Q LOSS WILD-TYPE 176  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    262  136
  18Q LOSS WILD-TYPE  176   26
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON               262                176
  RECTUM              136                 26
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q LOSS MUTATED        57        0       20       104         4         3
  18Q LOSS WILD-TYPE      45        1       16        67         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          13         16         57         41       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
D72V4, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  57                 45
  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               57                 21
  STAGE IIIC               41                 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  65 281  43
  18Q LOSS WILD-TYPE   9  40 131  22
D72V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               11                  9
  T2               65                 40
  T3              281                131
  T4               43                 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   201 111  86
  18Q LOSS WILD-TYPE 140  37  26
D72V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              201                140
  N1              111                 37
  N2               86                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  18Q LOSS MUTATED   283  65   9   1  39
  18Q LOSS WILD-TYPE 163   9   1   1  24
D72V7, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               283                163
  M1                65                  9
  M1A                9                  1
  M1B                1                  1
  MX                39                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   184 217
  18Q LOSS WILD-TYPE  99 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    184  217
  18Q LOSS WILD-TYPE   99  104
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              184                 99
  MALE                217                104
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                    246                            15
  18Q LOSS WILD-TYPE                  132                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                     125                             10
  18Q LOSS WILD-TYPE                    21                              3
D72V9, multiclass
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        246                132
  COLON MUCINOUS ADENOCARCINOMA                15                 44
  RECTAL ADENOCARCINOMA                       125                 21
  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"
D72V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     8 393
  18Q LOSS WILD-TYPE   1 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8  393
  18Q LOSS WILD-TYPE    1  202
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 8                  1
  YES              393                202
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   287   3  30  14
  18Q LOSS WILD-TYPE 149   2   6  15
D72V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              287                149
  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"
D72V12, 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                          38   199
  18Q LOSS WILD-TYPE                        18    93
D72V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  6
  BLACK OR AFRICAN AMERICAN                      38                 18
  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(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    41  17
  19P LOSS WILD-TYPE 425  92
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                58                517 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                 92 
$`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         0.99        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        48.20        13.05        14.99 
TCGA-D5-6533 TCGA-D5-6537 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6808 TCGA-G4-6295 
        1.32         4.50        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        14.86        18.28 

$`19P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        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        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        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         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
        2.01        12.99        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-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        17.03         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-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        32.02        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-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-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         1.58         1.02         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         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         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        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 
        8.02        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         7.92 
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         1.28 
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        43.07        61.87        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         4.11        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       26.99        17.29         6.64        14.76        67.00        17.95 
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-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39         8.45        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         1.02         2.01        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-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-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-A01L TCGA-AG-A01N 
       37.02        15.95        36.03         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        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         4.60         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        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.00        15.02        36.00         7.10 
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-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       41.36        57.24       129.27        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-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 
       16.31        16.41         8.61        10.78        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        37.51         0.39         1.02         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 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.20               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            102.44             140.38 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            16.685             17.950 
[1] "0.2 - 102.4 (16.7)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.7"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    40  22
  19P LOSS WILD-TYPE 398 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     40   22
  19P LOSS WILD-TYPE  398  140
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON                40                398
  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      94        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         72         44       51
                    vv
clus                 STAGE IVA STAGE IVB
  19P LOSS MUTATED           7         1
  19P LOSS WILD-TYPE        20         1
D73V4, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   8                 94
  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                 72
  STAGE IIIC                9                 44
  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  96 367  57
D73V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 19
  T2                9                 96
  T3               45                367
  T4                8                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19P LOSS MUTATED    24  16  23
  19P LOSS WILD-TYPE 317 132  89
D73V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               24                317
  N1               16                132
  N2               23                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  19P LOSS MUTATED    38  13   3   1   7
  19P LOSS WILD-TYPE 408  61   7   1  56
D73V7, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                38                408
  M1                13                 61
  M1A                3                  7
  M1B                1                  1
  MX                 7                 56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    30  33
  19P LOSS WILD-TYPE 253 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     30   33
  19P LOSS WILD-TYPE  253  288
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               30                253
  MALE                 33                288
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                     32                             7
  19P LOSS WILD-TYPE                  346                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                      21                              0
  19P LOSS WILD-TYPE                   125                             13
D73V9, multiclass
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         32                346
  COLON MUCINOUS ADENOCARCINOMA                 7                 52
  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"
D73V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  61
  19P LOSS WILD-TYPE   7 534
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   61
  19P LOSS WILD-TYPE    7  534
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                  7
  YES               61                534
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    41   0   6   3
  19P LOSS WILD-TYPE 395   5  30  26
D73V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               41                395
  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"
D73V12, 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                        51   262
D73V13, 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                 51
  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(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    38  13
  19Q LOSS WILD-TYPE 428  96
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                51                524 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                 96 
$`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         0.99        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        48.20        13.05 
TCGA-D5-5537 TCGA-D5-6533 TCGA-DM-A1DB TCGA-DM-A285 TCGA-F4-6704 TCGA-F4-6808 
       14.99         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        14.86        18.28 

$`19Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 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 
       52.44         9.63         5.03         1.02         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-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        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-3558 
       21.01        13.02        24.00        17.95        29.95        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-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         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-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-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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         8.02 
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         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        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         1.28         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        43.07        61.87        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         4.11        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        5.98         5.59         1.32         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        14.76        67.00        17.95        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-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
        8.45        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 
        1.02         2.01        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-3609 
        2.01        50.04        12.03         6.05         0.99        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        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-A014 
       20.98        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-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 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        9.37        13.97        60.03         7.99        11.01        15.02 
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         7.10        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-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45         9.96        37.51         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            102.44             140.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            18.280             17.805 
[1] "0.5 - 102.4 (18.3)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.5"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    35  19
  19Q LOSS WILD-TYPE 403 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     35   19
  19Q LOSS WILD-TYPE  403  143
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON                35                403
  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      95        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         73         45       54
                    vv
clus                 STAGE IVA STAGE IVB
  19Q LOSS MUTATED           5         1
  19Q LOSS WILD-TYPE        22         1
D74V4, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   7                 95
  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                 73
  STAGE IIIC                8                 45
  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  98 371  59
D74V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 19
  T2                7                 98
  T3               41                371
  T4                6                 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
  19Q LOSS MUTATED    25  10  20
  19Q LOSS WILD-TYPE 316 138  92
D74V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               25                316
  N1               10                138
  N2               20                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  19Q LOSS MUTATED    37   9   2   1   6
  19Q LOSS WILD-TYPE 409  65   8   1  57
D74V7, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                37                409
  M1                 9                 65
  M1A                2                  8
  M1B                1                  1
  MX                 6                 57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29  26
  19Q LOSS WILD-TYPE 254 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   26
  19Q LOSS WILD-TYPE  254  295
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               29                254
  MALE                 26                295
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                     28                             6
  19Q LOSS WILD-TYPE                  350                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                      18                              0
  19Q LOSS WILD-TYPE                   128                             13
D74V9, multiclass
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         28                350
  COLON MUCINOUS ADENOCARCINOMA                 6                 53
  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"
D74V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  53
  19Q LOSS WILD-TYPE   7 542
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   53
  19Q LOSS WILD-TYPE    7  542
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 2                  7
  YES               53                542
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    39   0   4   3
  19Q LOSS WILD-TYPE 397   5  32  26
D74V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               39                397
  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"
D74V12, 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                        52   268
D74V13, 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                 52
  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(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    51  11
  20P LOSS WILD-TYPE 415  98
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                62                513 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                 98 
$`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         7.92        12.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
       92.75        49.91         1.28         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        10.52         5.19        30.28        14.50 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-4022 
       86.63        11.84        36.03        32.02         6.05         0.99 
TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.94         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-DC-6683 TCGA-DY-A1DD TCGA-EI-6881 TCGA-F5-6571 
        1.94        38.96        10.06        57.24        16.41        31.30 
TCGA-F5-6702 TCGA-F5-6864 
       14.86         0.46 

$`20P LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
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-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-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        33.07        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-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-6899 
       21.37         4.21        56.55         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         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-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
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        48.20        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 
        8.02        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 
       14.99        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         4.50        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        43.07        61.87        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         4.11        10.98         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         1.32         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        67.00        24.13        17.95        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-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 
        8.45        15.39        20.02        10.39        65.98        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        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-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-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 
       37.02        15.95        36.03         9.07        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97        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         4.60         1.81        10.19         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        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        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         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
       13.05         5.29       126.44        41.36       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-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-F5-6810 TCGA-F5-6811 
       11.97         8.45         9.96        37.51         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.46               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             92.75             140.38 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             22.01              17.75 
[1] "0.5 - 92.8 (22.0)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    42  22
  20P LOSS WILD-TYPE 396 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     42   22
  20P LOSS WILD-TYPE  396  140
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON                42                396
  RECTUM               22                140
[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        17         0         1
  20P LOSS WILD-TYPE      94        1       29       154        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          1         13          6        6
  20P LOSS WILD-TYPE        23         20         65         47       55
                    vv
clus                 STAGE IVA STAGE IVB
  20P LOSS MUTATED           3         0
  20P LOSS WILD-TYPE        24         2
D75V4, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   8                 94
  STAGE IA                  0                  1
  STAGE II                  7                 29
  STAGE IIA                17                154
  STAGE IIB                 0                 10
  STAGE IIC                 1                  2
  STAGE III                 3                 23
  STAGE IIIA                1                 20
  STAGE IIIB               13                 65
  STAGE IIIC                6                 47
  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     0  10  47   8
  20P LOSS WILD-TYPE  20  95 365  57
D75V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                 20
  T2               10                 95
  T3               47                365
  T4                8                 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
  20P LOSS MUTATED    34  20  11
  20P LOSS WILD-TYPE 307 128 101
D75V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               34                307
  N1               20                128
  N2               11                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  20P LOSS MUTATED    49   8   0   0   8
  20P LOSS WILD-TYPE 397  66  10   2  55
D75V7, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                49                397
  M1                 8                 66
  M1A                0                 10
  M1B                0                  2
  MX                 8                 55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    33  32
  20P LOSS WILD-TYPE 250 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     33   32
  20P LOSS WILD-TYPE  250  289
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               33                250
  MALE                 32                289
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                     38                             4
  20P LOSS WILD-TYPE                  340                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                      20                              2
  20P LOSS WILD-TYPE                   126                             11
D75V9, multiclass
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         38                340
  COLON MUCINOUS ADENOCARCINOMA                 4                 55
  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"
D75V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  65
  20P LOSS WILD-TYPE   9 530
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   65
  20P LOSS WILD-TYPE    9  530
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  9
  YES               65                530
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    49   1   5   2
  20P LOSS WILD-TYPE 387   4  31  27
D75V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               49                387
  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"
D75V12, 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    28
  20P LOSS WILD-TYPE                        49   264
D75V13, 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                 49
  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(76) Variable = 20Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 462 107
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                569 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                107 
$`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         7.92        92.75        10.52 

$`20Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        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        15.52        37.05        37.25        16.04        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-A6-6649 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        52.44         9.63         5.03         1.02         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-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-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-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-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        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-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-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        17.03         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         0.99        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         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        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        48.20        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         8.02        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        14.99 
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         4.50 
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         1.28 
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        43.07        61.87        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 
        4.11        10.98         2.79         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        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 
        8.45        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 
        1.02         2.01        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-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         4.60         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        60.03         7.99        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         7.10 
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-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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.75             140.38 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              9.22              17.95 
[1] "2.0 - 92.8 (9.2)"   "0.1 - 140.4 (17.9)"
[1] "hr=" "1.8"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 432 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  432  162
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON                 6                432
  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     102        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         77         52       61
                    vv
clus                 STAGE IVA STAGE IVB
  20Q LOSS MUTATED           0         0
  20Q LOSS WILD-TYPE        27         2
D76V4, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                102
  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                 77
  STAGE IIIC                1                 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
  20Q LOSS MUTATED     0   0   6   0
  20Q LOSS WILD-TYPE  20 105 406  65
D76V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                 20
  T2                0                105
  T3                6                406
  T4                0                 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
  20Q LOSS MUTATED     3   1   2
  20Q LOSS WILD-TYPE 338 147 110
D76V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                3                338
  N1                1                147
  N2                2                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"
                    vv
clus                  M0  M1 M1A M1B  MX
  20Q LOSS MUTATED     6   0   0   0   0
  20Q LOSS WILD-TYPE 440  74  10   2  63
D76V7, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                 6                440
  M1                 0                 74
  M1A                0                 10
  M1B                0                  2
  MX                 0                 63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   3
  20Q LOSS WILD-TYPE 280 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    3
  20Q LOSS WILD-TYPE  280  318
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                280
  MALE                  3                318
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                      5                             1
  20Q LOSS WILD-TYPE                  373                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                       0                              0
  20Q LOSS WILD-TYPE                   146                             13
D76V9, multiclass
                                clus
vv                               20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          5                373
  COLON MUCINOUS ADENOCARCINOMA                 1                 58
  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"
D76V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   6
  20Q LOSS WILD-TYPE   9 589
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    6
  20Q LOSS WILD-TYPE    9  589
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                  9
  YES                6                589
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   0   0   0
  20Q LOSS WILD-TYPE 431   5  36  29
D76V11, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                431
  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"
D76V12, 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                        54   290
D76V13, 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                 54
  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(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   145  33
  21Q LOSS WILD-TYPE 321  76
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               178                397 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                33                 76 
$`21Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5665 
       37.02        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         0.99        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 
       14.93         0.99         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 
       17.03        27.02        42.02        21.99        15.02         0.99 
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 
        1.02         0.20         0.43        14.50        16.31         0.20 
TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.52         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        48.20 
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        14.99        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         4.11         5.98 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 
        5.19        26.99        24.13        17.95        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         1.02        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         7.10 
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-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
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        15.52 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        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 
       52.44         1.02         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-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 
       24.03        37.05        36.03         8.05        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99         0.99        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-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-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98         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 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95        17.03        33.07        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       31.07        31.07        53.00        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G 
        0.99        17.03        14.99        34.98        15.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        26.01        37.02        39.06         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.72         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        0.10         0.76         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       15.75        21.44        17.82         5.19         6.87        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         8.02        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 
        7.92        15.12        17.85         4.50        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         1.28        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        43.07        61.87 
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        10.52         2.79         5.59         1.32 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        5.49        17.29         6.64        14.76        30.28        67.00 
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-5654 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 
        8.45        65.98        36.03        32.02         8.02         2.01 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        1.02         2.01        50.04         0.99        15.95        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-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
        1.02        36.95        13.02        35.01        14.01        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         1.02         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-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A032 
        9.07         1.02        51.98        49.97         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 
       30.05        12.95         5.29        41.36        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 
        2.40        19.96        17.00        18.28        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        37.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
       14.86         1.02         0.69         1.12         0.46        55.76 
TCGA-G5-6572 
       47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.20               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            140.38             139.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             17.85              17.82 
[1] "0.2 - 140.4 (17.9)" "0.1 - 139.2 (17.8)"
[1] "hr=" "1"  
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   122  67
  21Q LOSS WILD-TYPE 316  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    122   67
  21Q LOSS WILD-TYPE  316   95
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON               122                316
  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      75        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         51         31       37
                    vv
clus                 STAGE IVA STAGE IVB
  21Q LOSS MUTATED           7         0
  21Q LOSS WILD-TYPE        20         2
D77V4, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  27                 75
  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                 51
  STAGE IIIC               22                 31
  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  71 280  47
D77V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                6                 14
  T2               34                 71
  T3              132                280
  T4               18                 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
  21Q LOSS MUTATED    93  51  46
  21Q LOSS WILD-TYPE 248  97  66
D77V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               93                248
  N1               51                 97
  N2               46                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  21Q LOSS MUTATED   137  25   3   0  24
  21Q LOSS WILD-TYPE 309  49   7   2  39
D77V7, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               137                309
  M1                25                 49
  M1A                3                  7
  M1B                0                  2
  MX                24                 39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    92  98
  21Q LOSS WILD-TYPE 191 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     92   98
  21Q LOSS WILD-TYPE  191  223
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               92                191
  MALE                 98                223
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                    114                             8
  21Q LOSS WILD-TYPE                  264                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                      62                              3
  21Q LOSS WILD-TYPE                    84                             10
D77V9, multiclass
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        114                264
  COLON MUCINOUS ADENOCARCINOMA                 8                 51
  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"
D77V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 186
  21Q LOSS WILD-TYPE   5 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  186
  21Q LOSS WILD-TYPE    5  409
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  5
  YES              186                409
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   137   1  12   6
  21Q LOSS WILD-TYPE 299   4  24  23
D77V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              137                299
  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"
D77V12, 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                        41   197
D77V13, 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                 41
  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(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   143  41
  22Q LOSS WILD-TYPE 323  68
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               184                391 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                41                 68 
$`22Q LOSS MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       15.52        34.65        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       29.19        23.61        22.52        20.61        21.76        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         9.63         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       24.03        37.05        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 
       21.01        13.02        19.99        13.94         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 
       50.04        37.05        85.05         0.99        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 
       37.02        17.03         0.99        33.07        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       17.03        24.03        27.02        18.05         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01         2.01        21.99        50.99        13.05        26.01 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        13.94        34.03        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F 
       14.99        15.02        33.04        26.01        37.02        39.98 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00        40.96         1.58         1.02         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4323 TCGA-AZ-4614 
       14.50        16.31        15.75         5.52         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 
        3.06         0.26         1.35        48.20         2.01         8.02 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 
        8.02        29.06        30.08         5.03        15.02        15.02 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.01        14.99        13.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6929 
        7.92        15.12        17.85        12.49         7.53        13.41 
TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       11.38        12.59       140.38       131.51         6.12        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 
       13.38         1.55        16.24         1.28         8.35        82.39 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       45.11        36.72        36.00        91.79        46.75         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV TCGA-AF-2692 TCGA-AF-4110 
       10.98        10.52         5.98        26.99        13.55        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       15.39        10.39        65.98        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 
        2.01        34.03        29.98         1.02        19.99         1.02 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A01L 
        1.02        19.99        36.03        14.04        25.97        12.00 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 
       10.98         1.94        38.96         0.49         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 
        6.05         4.73        13.97        10.98        12.99        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG 
        7.10        30.05        13.05        10.06        41.36        51.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 
        2.40        20.55        17.69        16.41        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.76        18.28        26.43 

$`22Q LOSS WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       17.79        37.05        37.25        16.04        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         1.02         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-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       15.95        14.93        36.03         0.99        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       20.98        34.03        16.08        34.06        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-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        18.05        17.03         4.01         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-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-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.79         0.72         0.10         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
        5.19         6.87        75.25        50.37        58.39        32.94 
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-6606 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
        6.77       100.01        11.74         2.24         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.33         0.10        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-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-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.03        22.98        16.01        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.26        19.59        11.51        20.42        17.75        18.25 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
        4.50        17.13        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       92.75        49.91        13.32         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-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       55.04        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-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
        2.79         5.59         1.32         5.19         5.49        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        6.64        14.76        30.28        67.00        24.13        17.95 
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-A56N TCGA-AG-3574 TCGA-AG-3580 
        8.45        20.02        86.63        11.84        36.03         8.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        1.02        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-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-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        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-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.04         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       11.01        15.02        12.00        15.02        36.00        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        0.49        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
        1.02         0.69         0.53         1.12         0.46        55.76 
TCGA-G5-6572 
       47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.38             139.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             15.02              19.07 
[1] "0.2 - 140.4 (15.0)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.6"
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   139  55
  22Q LOSS WILD-TYPE 299 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    139   55
  22Q LOSS WILD-TYPE  299  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON               139                299
  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        23        0        9        46         1         1
  22Q LOSS WILD-TYPE      79        1       27       125         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           9         11         28         21       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
D78V4, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  23                 79
  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               28                 50
  STAGE IIIC               21                 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  30 136  26
  22Q LOSS WILD-TYPE  16  75 276  39
D78V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                 16
  T2               30                 75
  T3              136                276
  T4               26                 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  66  44
  22Q LOSS WILD-TYPE 256  82  68
D78V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               85                256
  N1               66                 82
  N2               44                 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"
                    vv
clus                  M0  M1 M1A M1B  MX
  22Q LOSS MUTATED   132  36   4   0  21
  22Q LOSS WILD-TYPE 314  38   6   2  42
D78V7, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               132                314
  M1                36                 38
  M1A                4                  6
  M1B                0                  2
  MX                21                 42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    90 106
  22Q LOSS WILD-TYPE 193 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     90  106
  22Q LOSS WILD-TYPE  193  215
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               90                193
  MALE                106                215
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                    130                             9
  22Q LOSS WILD-TYPE                  248                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                      51                              4
  22Q LOSS WILD-TYPE                    95                              9
D78V9, multiclass
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        130                248
  COLON MUCINOUS ADENOCARCINOMA                 9                 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"
D78V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 192
  22Q LOSS WILD-TYPE   5 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  192
  22Q LOSS WILD-TYPE    5  403
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 4                  5
  YES              192                403
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   133   2  15  11
  22Q LOSS WILD-TYPE 303   3  21  18
D78V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              133                303
  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"
D78V12, 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                          19    91
  22Q LOSS WILD-TYPE                        37   201
D78V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  9
  BLACK OR AFRICAN AMERICAN                      19                 37
  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(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    56  16
  XQ LOSS WILD-TYPE 410  93
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               72               503 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16                93 
$`XQ LOSS MUTATED`
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-A567 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       42.28        35.11        61.84        38.99         9.07        37.05 
TCGA-AA-3548 TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3837 TCGA-AA-3860 TCGA-AA-3941 
       33.99        19.99        15.02        38.99        31.07        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00D 
        2.01         2.01        21.99        24.00         7.96        19.00 
TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02F TCGA-AD-6965 TCGA-AU-3779 
        0.99        32.02        31.00        39.98         0.20        14.50 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CK-5912 
       15.75         5.52        11.74         3.19         3.29        48.20 
TCGA-CK-6748 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A0XD 
        2.01        15.02        11.01        14.99        12.00        24.43 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6808 TCGA-G4-6295 
       49.91       140.38       131.51        26.47        33.67         8.35 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 
       61.87        36.72        26.04        10.98         5.98         5.49 
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-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 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       23.38        17.79        44.91        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        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        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         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-3530 
        1.02        24.03        36.03         8.05        19.07        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-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 
        0.99         0.99        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-3846 
       17.98        15.95        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       26.01        25.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        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         0.99        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-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         1.58         1.02         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.46         0.92        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         6.87        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-6608 TCGA-CA-5254 
       12.10       100.01        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-6751 
       15.62        51.32        21.99        21.14         2.93       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         8.02        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-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        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-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.41         1.51        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 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         1.28 
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-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        74.56        43.07        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       47.15        52.80         4.11        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        12.72        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 
       15.39        20.02        10.39        86.63        65.98        36.03 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         1.02         2.01         1.02        46.03 
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-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-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        70.03        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.94        38.96        61.97        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         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-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48         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-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         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 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.20              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           140.38            139.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            22.50             17.56 
[1] "0.2 - 140.4 (22.5)" "0.1 - 139.2 (17.6)"
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    49  27
  XQ LOSS WILD-TYPE 389 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     49   27
  XQ LOSS WILD-TYPE  389  135
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON               49               389
  RECTUM              27               135
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ LOSS MUTATED        11        0        5        21         0         0
  XQ LOSS WILD-TYPE      91        1       31       150        10         3
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           1          2          7         10       15
  XQ LOSS WILD-TYPE        25         19         71         43       46
                   vv
clus                STAGE IVA STAGE IVB
  XQ LOSS MUTATED           3         0
  XQ LOSS WILD-TYPE        24         2
D79V4, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 11                91
  STAGE IA                 0                 1
  STAGE II                 5                31
  STAGE IIA               21               150
  STAGE IIB                0                10
  STAGE IIC                0                 3
  STAGE III                1                25
  STAGE IIIA               2                19
  STAGE IIIB               7                71
  STAGE IIIC              10                43
  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  54   9
  XQ LOSS WILD-TYPE  19  92 358  56
D79V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                19
  T2              13                92
  T3              54               358
  T4               9                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    39  18  20
  XQ LOSS WILD-TYPE 302 130  92
D79V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              39               302
  N1              18               130
  N2              20                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"
                   vv
clus                 M0  M1 M1A M1B  MX
  XQ LOSS MUTATED    51  17   2   0   6
  XQ LOSS WILD-TYPE 395  57   8   2  57
D79V7, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               51               395
  M1               17                57
  M1A               2                 8
  M1B               0                 2
  MX                6                57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    36  41
  XQ LOSS WILD-TYPE 247 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     36   41
  XQ LOSS WILD-TYPE  247  280
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              36               247
  MALE                41               280
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                     43                             6
  XQ LOSS WILD-TYPE                  335                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                      23                              4
  XQ LOSS WILD-TYPE                   123                              9
D79V9, multiclass
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        43               335
  COLON MUCINOUS ADENOCARCINOMA                6                53
  RECTAL ADENOCARCINOMA                       23               123
  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
  XQ LOSS MUTATED     1  76
  XQ LOSS WILD-TYPE   8 519
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   76
  XQ LOSS WILD-TYPE    8  519
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 8
  YES              76               519
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    50   0   7   4
  XQ LOSS WILD-TYPE 386   5  29  25
D79V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              50               386
  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"
D79V12, 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                           8    31
  XQ LOSS WILD-TYPE                        48   261
D79V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                10
  BLACK OR AFRICAN AMERICAN                      8                48
  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"
