[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"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[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_mergedClustering/COADREAD-TP/11592014/COADREAD-TP.mergedcluster.txt"

nPatients in clinical file=620, in cluster file=628, common to both=617
[1]  12 617
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
46 62 72 42 
 1  2  3  4 
46 62 72 42 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
52 41 77 52 
 1  2  3  4 
52 41 77 52 
[1] "CN_CNMF"
[1] 3
  1   2   3 
250 203 151 
  1   2   3 
250 203 151 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 98 158 120 
  1   2   3 
 98 158 120 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
100 179  42 140 
  1   2   3   4 
100 179  42 140 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 54 307 100 
  1   2   3 
 54 307 100 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
139 131 135 196 
  1   2   3   4 
139 131 135 196 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 79 121  96  63 153  39  50 
  1   2   3   4   5   6   7 
 79 121  96  63 153  39  50 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
212  96 241 
  1   2   3 
212  96 241 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
229 144 176 
  1   2   3 
229 144 176 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
24 20 29 28 18 17 
 1  2  3  4  5  6 
24 20 29 28 18 17 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
55 15 34 32 
 1  2  3  4 
55 15 34 32 
[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 617 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-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
        1014          996         1111           NA          987         1001 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
         962          926          888         1020          718          672 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
         671          995          887          824          685          734 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
         255          763          766          735          627          662 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
         751          742          726          612          598          617 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
          NA           NA           NA         1595          293           NA 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
          31           NA           31         1127           31         1065 
TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1765         1915         1946          212           31           NA 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 
        1186           31          276          731           NA         1127 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 
        1096          245          580           NA           NA          580 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        1035          882          882          791          395           30 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
         426         1034          639           NA          730          546 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
         911          700          638          608          424          608 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
        1856         2375          184          212         1643           NA 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
         426           28         1522         1431         1430          457 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
          NA          182           NA         1127          578           NA 
TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 
          NA           NA           NA         2587          821           NA 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3815 
         579           30           30         1066           NA         1005 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
          NA          761           31          547          485         1186 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
        1124         1126          454           NA          518           30 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
          NA         1006           NA         1096          975           30 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 
         945          945           NA          914         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-3970 
          NA          638         1035           61          669         1096 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
         489         1551          397         1036          791          761 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 
         730          822          822           NA          580           NA 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
         822          424         1157          578          913         1035 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
         549          549          518           NA          822         1278 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
          30          518          456          669         1064          457 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
         457           30          974          365          943          943 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
          NA           31         1065           31         1005         1065 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
         791         1126           NA           NA         1581           NA 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R 
        1216           NA           NA           NA           28           NA 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        1247         1216           NA         1246            2          650 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
         128         1720           24           22           48           31 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 
           3           23            6           NA           13           14 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
          28          441          824           NA           NA          479 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
           6          652          542          158          168          209 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        2289         1532         1776           NA           NA         1002 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
          NA         2549           NA         1977           NA         1868 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
          NA           NA           NA           68           93           65 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
          99          100            2            8           10            3 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
          41          534         3116         1227         2134          475 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 
        1466         1561          669           NA           NA           NA 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
          89           61         3780          701          609         1126 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
         244          792          244          822          396          884 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
         670          699          915          487          457           NA 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
         457          457          518          457          365          427 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
         883          488          669          456          395          396 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
         457          427          335          394          397          337 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
         337          335          306          366          456          373 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
         596          411          350          614          621          540 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
         555           40          241          460          543          137 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
         521          380          491          474          229          377 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
         308          378          435          275          287          354 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
         408           46          365          346          312         3641 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
         743         1162         3974         2821         1518          405 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
         383         4270          228         1348         4000         4126 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
         236         4233          186          427          805         2475 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
        3648         1094         1849         3561         2988         2895 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
          NA          407           NA          415          409           NA 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        1091           47          496          900          494         1024 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
          39           16         1077          591         3275           NA 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
         254         2506           NA         2268         1310         1882 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
        1631         1359         1674         1574         1372         1199 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
        1093         1117         1095          804          672          792 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
         419         1089          796         2792           NA         1434 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
        1606          125           NA          320           85          182 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
         170           40          158          167          821          526 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
         202          449          921         2038          734          546 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
         524         1309          412          581          387         1148 
TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
          NA         1146          441          257          468          609 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
         316         2635         2007          360           NA          365 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
         974          244          215           31           61           NA 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
          31         1400           NA           NA         1035           NA 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 
        1522          366          184           NA           NA           30 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
         485          608           NA          608           NA          243 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
          30          912           31         1003           30           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
          NA          608           31           NA         1124          518 
TCGA-AG-3891 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
         548          396         1065          426           31         1461 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
          NA          974          608          853         1096          427 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
          31          518           NA           NA           30          638 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
         424          183          790          700         1126          485 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
        1096          276           31          365          943         2130 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        1947          334           NA         1520           NA           NA 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
        1885         1247         1157         3562           15           44 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
           6           21           22          140           55          310 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
         184          184           NA          212          285          144 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
         425         1826          243          334          335          457 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
         395          365          425          457         1095          216 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
         914          394          397          306          161         3846 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        1258         1741         3932          734         1566          992 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
          15           73          625          607          636          517 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
         556          482          538          497          496          499 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
         262          350          328          415          531          364 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
         257           NA         1141          952          452           12 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
          31           20           21           16           34           23 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          14           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=98,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=351,	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 617 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 
 20 107 421  67 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 107 421  67 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 107 421  67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 107 421  67 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
350 148 115 
[1] "table(vv)"
vv
 N0  N1  N2 
350 148 115 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
350 148 115 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
350 148 115 
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 = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 32  8
  subtype2 43 15
  subtype3 58  8
  subtype4 34  5
subtype1 subtype2 subtype3 subtype4 
      40       58       66       39 
subtype1 subtype2 subtype3 subtype4 
       8       15        8        5 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
       46.65        43.76        23.38        33.34        32.75        36.53 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 
        1.02        13.02        24.03         0.99        17.95         0.92 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3842 
       26.99         0.99         0.99        33.04        15.95        37.02 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        17.03        27.02        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
       33.01        26.01        24.00         2.01        25.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A02R TCGA-AF-3400 
       19.00        30.02         0.99         0.99        22.03        12.72 
TCGA-AG-3575 TCGA-AG-3600 TCGA-AG-3878 TCGA-AG-3883 
       12.00         6.05         0.99         1.02 

$subtype2
TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 
       17.79        15.52        34.65        38.99         9.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3696 TCGA-AA-3837 TCGA-AA-3875 
       24.00        19.99         2.01         5.03        38.99        18.05 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-A00L TCGA-AA-A00O 
        2.01        50.99        13.05        26.01        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A02E 
       42.02        21.99        15.02        15.02        31.00         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 TCGA-AF-3913 
       39.98         2.01         5.03        41.00        16.31        10.39 
TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3890 
       36.03        24.00        19.99        19.99         7.99        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
        1.02        17.03        15.95         9.07         1.02        31.00 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       51.98         1.94        38.96        38.04 

$subtype3
TCGA-A6-2678 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3552 TCGA-AA-3562 
       42.28        36.03        19.07        29.00        13.02        19.99 
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-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3841 
       36.00        35.05         0.99        25.02        17.98        36.95 
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-3862 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3955 TCGA-AA-3956 
       31.07        30.05        24.03        12.99        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 
       21.99        36.03        16.08        34.06        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00W TCGA-AY-4071 
       27.02        19.07         7.96        34.03        14.99         0.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       43.04        13.55        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        2.01         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3896 
        0.99        15.95         0.99        29.98        19.99         1.02 
TCGA-AG-3909 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A025 
       19.99         6.02        23.01        37.02        12.00        49.97 

$subtype4
TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3556 
        1.02        37.05         8.05        19.07        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
       20.98        13.94        54.02        47.05        11.01         5.98 
TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3994 TCGA-AA-A004 
        1.02        36.03        53.00        24.00        27.02        13.94 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01F 
       18.05        18.05         4.01        17.03        34.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01Q TCGA-AA-A024 TCGA-AA-A029 TCGA-AF-2689 
       12.00        31.00         1.02        39.06        51.98        17.95 
TCGA-AG-3594 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A008 
        2.01        36.95        13.02        32.02        20.98        13.94 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A02X 
       25.97        36.03        41.00 

subtype1 subtype2 subtype3 subtype4 
    0.92     1.02     0.95     1.02 
subtype1 subtype2 subtype3 subtype4 
   46.65    51.98    50.04    54.02 
subtype1 subtype2 subtype3 subtype4 
  22.705   19.990   20.485   20.980 
[1] "0.9 - 46.6 (22.7)" "1.0 - 52.0 (20.0)" "0.9 - 50.0 (20.5)"
[4] "1.0 - 54.0 (21.0)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 39  7
  subtype2 37 25
  subtype3 45 25
  subtype4 31 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    7
  subtype2   37   25
  subtype3   45   25
  subtype4   31   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        39       37       45       31
  RECTUM        7       25       25       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       8        3        15         3         3          1          4
  subtype2       9        2        14         0         2          2          5
  subtype3      19        4        23         0         4          0          7
  subtype4      11        6        13         2         1          0          6
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        6         0
  subtype2         11       17         0
  subtype3          7        8         0
  subtype4          0        2         1
D1V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           8        9       19       11
  STAGE II          3        2        4        6
  STAGE IIA        15       14       23       13
  STAGE IIB         3        0        0        2
  STAGE III         3        2        4        1
  STAGE IIIA        1        2        0        0
  STAGE IIIB        4        5        7        6
  STAGE IIIC        2       11        7        0
  STAGE IV          6       17        8        2
  STAGE IVA         0        0        0        1
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  9 30  6
  subtype2  1 12 41  8
  subtype3  5 16 51  0
  subtype4  2  9 26  5
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        1        5        2
  T2        9       12       16        9
  T3       30       41       51       26
  T4        6        8        0        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 30  6 10
  subtype2 28 17 17
  subtype3 46 12 14
  subtype4 32  8  2
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       30       28       46       32
  N1        6       17       12        8
  N2       10       17       14        2
[1] 3 4
[1] 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
  subtype1 39  6   0
  subtype2 45 17   0
  subtype3 63  8   0
  subtype4 39  2   1
D1V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        39       45       63       39
  M1         6       17        8        2
  M1A        0        0        0        1
[1] 3 4
[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
  subtype1 28 18
  subtype2 33 29
  subtype3 30 42
  subtype4 15 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   18
  subtype2   33   29
  subtype3   30   42
  subtype4   15   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28       33       30       15
  MALE         18       29       42       27
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   28                            11
  subtype2                   36                             1
  subtype3                   44                             1
  subtype4                   21                             9
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     4                              2
  subtype2                    25                              0
  subtype3                    21                              2
  subtype4                     8                              3
D1V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 28       36       44       21
  COLON MUCINOUS ADENOCARCINOMA        11        1        1        9
  RECTAL ADENOCARCINOMA                 4       25       21        8
  RECTAL MUCINOUS ADENOCARCINOMA        2        0        2        3
[1] 4 4
[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
  subtype1  1 45
  subtype2  0 62
  subtype3  0 72
  subtype4  0 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    0   62
  subtype3    0   72
  subtype4    0   42
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        0        0
  YES       45       62       72       42
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 38  0  4
  subtype2 45  2 15
  subtype3 62  0  8
  subtype4 40  0  2
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       38       45       62       40
  R1        0        2        0        0
  R2        4       15        8        2
[1] 3 4
[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       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     7
  subtype2                         2     3
  subtype3                         0     4
  subtype4                         0     1
D1V13, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       7        5        4        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                            7        3        4
[1] 2 3
[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 = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 37  9
  subtype2 28 11
  subtype3 60 11
  subtype4 42  5
subtype1 subtype2 subtype3 subtype4 
      46       39       71       47 
subtype1 subtype2 subtype3 subtype4 
       9       11       11        5 
$subtype1
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3514 
       46.65        43.76        23.38        33.34        32.75         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3543 TCGA-AA-3554 
       13.02         1.02         8.05        19.07         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       29.95        23.01         0.92        26.99         0.99         0.99 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3854 TCGA-AA-3864 
       33.04         1.02        15.95        37.02        36.03        53.00 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       29.98        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        27.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A02R 
       18.05         4.01         0.99         0.99         1.02        22.03 
TCGA-AF-3400 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-A02X 
       12.72         2.01         6.05        41.00 

$subtype2
TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3544 
       17.79        34.65        36.53        34.03        12.99        14.01 
TCGA-AA-3553 TCGA-AA-3696 TCGA-AA-3973 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       24.00         5.03        13.05        17.03        27.02        42.02 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A02E 
       21.99        34.98        15.02        15.02        31.00         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 TCGA-AF-3913 
       39.98         2.01         5.03        41.00        16.31        10.39 
TCGA-AG-3574 TCGA-AG-3584 TCGA-AG-3890 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 
       36.03        24.00        17.03        48.03        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       14.04         1.02        17.03         1.02        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
        1.94        38.96        38.04 

$subtype3
TCGA-A6-2678 TCGA-A6-2683 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       42.28        15.52         9.07        24.03        37.05        36.03 
TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3560 
       19.07        29.00        33.99        21.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       13.94        54.02         2.01        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       11.01         5.98        36.00         0.99        25.02        17.98 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3875 
       38.99        14.93         0.99        33.07        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       12.99        50.99        26.01        19.07         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G 
       19.00        18.05        17.03        14.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A024 TCGA-AA-A029 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       31.00        39.06        51.98        17.95        43.04        13.55 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       12.00        32.02         8.02         1.02        46.03        34.03 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       12.03         7.99         0.99        36.95        13.02        14.01 
TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       32.02        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07        51.98        49.97 

$subtype4
TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3667 
       38.99        29.00        26.01        13.02        19.99        14.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3846 
       15.02        37.05        19.00        35.05        36.95        17.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
       24.03         2.01        20.98        34.03        21.99        36.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-A00F 
       16.08        34.06        24.00        27.02        27.02        34.03 
TCGA-AY-4071 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3605 
        0.95         7.07         1.02         2.01        50.04         0.99 
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-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A011 
        1.02        35.01         1.02        19.99        37.02 

subtype1 subtype2 subtype3 subtype4 
    0.92     1.02     0.99     0.95 
subtype1 subtype2 subtype3 subtype4 
   53.00    48.03    54.02    50.04 
subtype1 subtype2 subtype3 subtype4 
   22.52    17.79    19.99    20.98 
[1] "0.9 - 53.0 (22.5)" "1.0 - 48.0 (17.8)" "1.0 - 54.0 (20.0)"
[4] "0.9 - 50.0 (21.0)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 46  6
  subtype2 24 17
  subtype3 48 28
  subtype4 34 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    6
  subtype2   24   17
  subtype3   48   28
  subtype4   34   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        46       24       48       34
  RECTUM        6       17       28       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        17         4         3          1          6
  subtype2       4        2        10         1         0          1          4
  subtype3      20        8        23         0         6          1          5
  subtype4      14        2        15         0         1          0          7
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        5         1
  subtype2          7       12         0
  subtype3          5        9         0
  subtype4          6        7         0
D2V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        4       20       14
  STAGE II          3        2        8        2
  STAGE IIA        17       10       23       15
  STAGE IIB         4        1        0        0
  STAGE III         3        0        6        1
  STAGE IIIA        1        1        1        0
  STAGE IIIB        6        4        5        7
  STAGE IIIC        2        7        5        6
  STAGE IV          5       12        9        7
  STAGE IVA         1        0        0        0
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 10 33  8
  subtype2  0  7 28  6
  subtype3  7 15 51  4
  subtype4  1 14 36  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        7        1
  T2       10        7       15       14
  T3       33       28       51       36
  T4        8        6        4        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 34  9  9
  subtype2 19 11 11
  subtype3 52 12 13
  subtype4 31 11 10
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       34       19       52       31
  N1        9       11       12       11
  N2        9       11       13       10
[1] 3 4
[1] 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
  subtype1 45  5   1
  subtype2 29 12   0
  subtype3 68  9   0
  subtype4 44  7   0
D2V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        45       29       68       44
  M1         5       12        9        7
  M1A        1        0        0        0
[1] 3 4
[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
  subtype1 30 22
  subtype2 22 19
  subtype3 34 43
  subtype4 20 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   22
  subtype2   22   19
  subtype3   34   43
  subtype4   20   32
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30       22       34       20
  MALE         22       19       43       32
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   27                            18
  subtype2                   24                             0
  subtype3                   44                             4
  subtype4                   34                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     2                              3
  subtype2                    17                              0
  subtype3                    23                              3
  subtype4                    16                              1
D2V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 27       24       44       34
  COLON MUCINOUS ADENOCARCINOMA        18        0        4        0
  RECTAL ADENOCARCINOMA                 2       17       23       16
  RECTAL MUCINOUS ADENOCARCINOMA        3        0        3        1
[1] 4 4
[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
  subtype1  1 51
  subtype2  0 41
  subtype3  0 77
  subtype4  0 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   51
  subtype2    0   41
  subtype3    0   77
  subtype4    0   52
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        0        0
  YES       51       41       77       52
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 45  0  3
  subtype2 28  2 11
  subtype3 69  0  8
  subtype4 43  0  7
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       45       28       69       43
  R1        0        2        0        0
  R2        3       11        8        7
[1] 3 4
[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       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     6
  subtype2                         2     3
  subtype3                         0     5
  subtype4                         0     1
D2V13, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       6        5        5        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                            6        3        5
[1] 2 3
[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 = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 189  49
  subtype2 162  31
  subtype3 115  29
subtype1 subtype2 subtype3 
     238      193      144 
subtype1 subtype2 subtype3 
      49       31       29 
$subtype1
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 
        5.06        46.65        43.76        23.38        42.28        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5664 
       37.05        37.25        16.04        14.53        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.06         8.38        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         1.02         3.02 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       58.03        63.98         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 
       37.05         8.05        19.07        29.00         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 
       29.95        23.01        61.02         6.97         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       11.01         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-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 
       38.99        14.93        36.03        32.05        53.00        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-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
        2.01         2.01        25.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       38.04        30.02        18.05         4.01        27.02         0.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       34.98         0.99        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R 
       35.01        35.01        26.01        39.06        51.98        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
        0.72         0.76         0.46         0.92        27.09         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.82         5.52        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 
        5.13        49.41         6.77        12.10       100.01         3.19 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.06         3.25         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      102.44        40.34        70.16        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5344 
      124.27        23.05        20.02        37.02        26.04        22.03 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.01        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 
       20.19        20.42        17.75         7.92        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       16.14        12.39        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 
        1.51        12.00        10.26        24.43        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       13.32       140.38       135.65         7.76       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       60.79        95.18        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 
       35.87         1.55        29.59        16.24        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      107.67        23.51        43.07        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       52.80         2.79         5.98        14.76        67.00        24.13 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 
       43.04        12.72         8.45        12.00         8.02         2.01 
TCGA-AG-3599 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       12.03         1.02         0.99        13.02        14.01        20.98 
TCGA-AG-A008 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
       13.94        10.98        49.97        61.97         0.49         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5337 
        4.60         1.81        10.19         6.05         4.73        15.02 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       30.05        12.95         5.29        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 
       20.91        18.28         8.61        10.78        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
        9.96         0.53         1.12        55.76 

$subtype2
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 
       37.02        44.91        35.11        45.60        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5666 
       36.53        32.45        32.91        30.44        23.61        32.71 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 
       22.52        24.13        25.08        20.61        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         5.03         6.97        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       34.03        14.01        21.01        19.99        13.94        19.99 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
        2.01        14.01        15.02        37.05        19.00        85.05 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 
       36.95        37.02        17.03         0.99         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       17.03        27.02        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       13.05        34.06        26.01        34.03        17.03        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        15.02        32.02        12.00 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6888 
       33.04         2.96        39.98         2.01        40.96         4.21 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
        1.02         0.10         0.43        14.50         0.95        15.75 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
        5.19         6.87        75.25        22.36        29.56         5.23 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        2.14         0.07        48.20        21.99         2.01         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
        8.02        13.02        16.01        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 
       29.03        16.04        15.02        11.08        10.06        19.59 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A1D8 
       13.51        18.25         1.32        15.12        11.38        12.59 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 
      131.51        14.04        26.47       119.93        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6297 
       13.38        33.67         1.28         0.53        28.21        82.39 
TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       61.87        45.11        36.72        91.79        46.75         4.11 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2689 
       10.52         1.32         5.19         5.49        26.99        17.95 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        37.74        10.39        14.50        15.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       86.63        11.84         7.07         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       50.04        15.95        19.99        19.99         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        0.99        19.99         1.02        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       48.03        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 
        0.99         6.02        25.97        23.01        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-CI-6622 TCGA-CI-6623 
       12.00        38.96        41.00        38.04         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       13.97         7.99        10.98        11.01        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       15.02        36.00        10.06       129.27        24.13        51.48 
TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 
        2.40        17.69        16.34        16.31        16.41        11.97 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       31.30         0.39         1.02         0.66         0.69         0.76 
TCGA-G5-6572 
       47.08 

$subtype3
TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5667 
        5.26        43.43        17.79        31.63        29.19        29.16 
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       27.09        25.18         9.63         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       35.01        36.03        19.07        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3662 
       33.99        13.02        24.00        20.98        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3851 
       54.02        50.04        47.01         5.98        36.00        33.07 
TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3979 
       31.07        24.03        29.98        24.00        34.03        24.00 
TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00U TCGA-AA-A01S 
       27.02        13.94        19.00        18.05        17.03         1.02 
TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6965 
       37.02         5.03         0.92        41.00         1.58         0.20 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       16.31        21.44         5.65        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 
       61.41        11.74         1.94         2.24         3.29         1.35 
TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       15.62        27.02        29.06        22.98        30.08         5.03 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5541 
       21.99        13.02        11.01        11.08        12.26        11.51 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.50        17.13        15.58         7.53        10.13        12.43 
TCGA-D5-6926 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB 
        9.04       119.70        38.20       130.65         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6805 TCGA-G4-6295 TCGA-G4-6299 
        6.12       117.07        98.24        16.31         8.35        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-NH-A50U 
       44.68        55.04        39.42        35.93        36.00        10.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-6655 
        5.59        17.29         6.64        30.28        17.23        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3586 
       10.39        65.98        36.03        32.02        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3887 
        2.01         6.05         0.99         7.99        32.98        36.95 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01N 
       32.02         1.02        37.02        15.95         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AH-6643 TCGA-AH-6644 
       70.03        64.01        51.98         1.94         0.69         0.72 
TCGA-CI-6619 TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA 
        6.05        60.03        13.97         7.10        13.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 
       41.36        57.24         0.49        17.00        15.85        11.51 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
       13.64        37.51        14.86         0.46        18.28        26.43 

subtype1 subtype2 subtype3 
    0.07     0.07     0.20 
subtype1 subtype2 subtype3 
  140.38   131.51   130.65 
subtype1 subtype2 subtype3 
  17.900   17.030   19.035 
[1] "0.1 - 140.4 (17.9)" "0.1 - 131.5 (17.0)" "0.2 - 130.7 (19.0)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1 207  43
  subtype2 128  71
  subtype3 103  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  207   43
  subtype2  128   71
  subtype3  103   48
        clus
vv       subtype1 subtype2 subtype3
  COLON       207      128      103
  RECTUM       43       71       48
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      52        1       18        82         6         0        11
  subtype2      32        0        5        54         3         1         9
  subtype3      18        0       13        35         1         2         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         26         18       15         7         1
  subtype2          7         33         14       26        13         1
  subtype3          7         19         21       20         7         0
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          52       32       18
  STAGE IA          1        0        0
  STAGE II         18        5       13
  STAGE IIA        82       54       35
  STAGE IIB         6        3        1
  STAGE IIC         0        1        2
  STAGE III        11        9        6
  STAGE IIIA        7        7        7
  STAGE IIIB       26       33       19
  STAGE IIIC       18       14       21
  STAGE IV         15       26       20
  STAGE IVA         7       13        7
  STAGE IVB         1        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  10  49 162  28
  subtype2   8  32 141  21
  subtype3   2  24 109  16
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       10        8        2
  T2       49       32       24
  T3      162      141      109
  T4       28       21       16
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 166  48  36
  subtype2 102  65  34
  subtype3  73  35  42
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      166      102       73
  N1       48       65       35
  N2       36       34       42
[1] 3 3
[1] 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
  subtype1 196  18   2   1  29
  subtype2 143  34   4   1  17
  subtype3 107  22   4   0  17
D3V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       196      143      107
  M1        18       34       22
  M1A        2        4        4
  M1B        1        1        0
  MX        29       17       17
[1] 5 3
[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
  subtype1 125 125
  subtype2  87 116
  subtype3  71  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125  125
  subtype2   87  116
  subtype3   71   80
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      125       87       71
  MALE        125      116       80
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  160                            46
  subtype2                  123                             5
  subtype3                   95                             8
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    33                              9
  subtype2                    71                              0
  subtype3                    42                              4
D3V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                160      123       95
  COLON MUCINOUS ADENOCARCINOMA        46        5        8
  RECTAL ADENOCARCINOMA                33       71       42
  RECTAL MUCINOUS ADENOCARCINOMA        9        0        4
[1] 4 3
[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
  subtype1   3 247
  subtype2   3 200
  subtype3   3 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  247
  subtype2    3  200
  subtype3    3  148
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        3
  YES      247      200      148
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 183   3   8  17
  subtype2 152   0  13   6
  subtype3 101   2  15   6
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      183      152      101
  R1        3        0        2
  R2        8       13       15
  RX       17        6        6
[1] 4 3
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                        23
  subtype2                                0     2                        21
  subtype3                                0     3                        12
          vv
clus       WHITE
  subtype1   127
  subtype2    93
  subtype3    72
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   7        2        3
  BLACK OR AFRICAN AMERICAN              23       21       12
  WHITE                                 127       93       72
[1] 4 3
[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 = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  81  16
  subtype2 122  33
  subtype3  92  23
subtype1 subtype2 subtype3 
      97      155      115 
subtype1 subtype2 subtype3 
      16       33       23 
$subtype1
TCGA-3L-AA1B TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5664 
        5.06        13.94        37.05        37.25        31.63        22.09 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 
        8.38        25.08        24.16        21.76        23.87        19.66 
TCGA-A6-A565 TCGA-AA-3489 TCGA-AA-3510 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6965 
       16.24         1.02        63.98        56.55         0.10         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AZ-4313 TCGA-AZ-4315 
       14.50        27.09        15.75         0.20        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
        1.41        62.79        12.10       100.01         5.23         3.19 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4748 
        3.06         0.33         0.10       102.44        23.05        26.04 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6167 
       22.98        30.08        15.02        12.00        14.04        14.99 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6536 TCGA-D5-6539 
       12.99        12.95        20.19        20.42        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
        7.53        14.30         9.04        11.64         1.51        11.38 
TCGA-DM-A280 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
        7.76        13.38        13.64        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       16.31        16.24         1.28        43.07        53.62        51.75 
TCGA-G4-6625 TCGA-G4-6627 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 
       91.79        47.15        24.13        17.23        19.10        14.50 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-A01Y TCGA-AH-6544 TCGA-AH-6547 
       20.02        10.39        32.98        64.01         0.49         1.45 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-6160 TCGA-DC-6681 
       10.19         6.05         9.37         4.73        30.05        12.95 
TCGA-DC-6682 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6884 TCGA-EI-6917 
       13.05        20.55        19.96        17.00        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6235 
        8.45         9.96        14.86         0.66         1.12        55.76 
TCGA-G5-6572 
       47.08 

$subtype2
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-3810 TCGA-A6-5656 
       37.02        43.43        17.79        35.11        36.53        32.91 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       29.19        23.61        32.71        29.16        27.09        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       25.18        20.61        24.69        20.28        61.84        52.44 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3509 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        62.96         6.97 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3697 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 
       61.02        78.08        85.05         4.21         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AZ-4308 TCGA-AZ-4681 
        1.02         0.76         0.43         0.46        75.25        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 
       22.36        65.00        29.56         1.94         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 
        0.07         1.35        48.20        21.99         2.01         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       13.02        29.06        22.03         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6172 
       15.02        29.03        16.04        21.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-5541 
       11.08        11.01        10.06        14.99        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6922 TCGA-DM-A0XF 
       18.25         1.32         7.92         4.50        10.13        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A 
      130.65        49.91        13.32        44.32       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6808 TCGA-F4-6854 
       81.37       119.93        35.97         8.61        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43        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-G4-6626 TCGA-NH-A50T TCGA-QG-A5YV TCGA-QG-A5YX 
       36.72        36.00        46.75         4.11        26.99        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
        6.64        30.28        37.74        15.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A036 
       11.84         0.99         0.99        10.98         1.94       117.11 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
        0.20         0.69         0.72         4.60         1.81         6.97 
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-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-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       32.61         2.40        15.85        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.51        13.64        11.97        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6641 
        1.02         0.69         0.76         0.46        26.43 

$subtype3
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-4107 
       44.91        45.60        16.04        32.75        14.53        32.45 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 
       30.44        33.53        22.06        22.52        24.39        20.12 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3662 
       24.92         9.63         3.02        35.01        58.03         6.05 
TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AM-5821 
        6.97        19.04         0.07        21.37         0.79         0.92 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4615 
       21.44        17.82         5.19         5.52         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 
        5.13        61.41        49.41         6.77        11.74         2.24 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        3.25         0.26        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       51.32        21.14         2.93       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6169 TCGA-CM-6171 
        8.02        27.02        16.01        15.02        13.02        14.04 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6531 
       13.05        11.08        12.03        12.26        19.59        17.75 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
       15.12        17.13        16.14        15.58        12.39        12.43 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.44        13.41        12.00        10.26       119.70        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
        6.12        14.04        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6320 
       11.11         6.18        29.59       107.67        74.56        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-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
       10.98        10.52         2.79         5.98         5.59        14.76 
TCGA-AG-3731 TCGA-AG-A01W TCGA-AG-A02N TCGA-CI-6620 TCGA-DT-5265 TCGA-DY-A1DF 
        1.02        70.03        61.97         6.05         5.29        24.13 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-F5-6814 
        0.49        20.91        18.28        17.69         8.61         0.53 
TCGA-G5-6233 
       18.28 

subtype1 subtype2 subtype3 
    0.10     0.07     0.07 
subtype1 subtype2 subtype3 
  102.44   139.17   140.38 
subtype1 subtype2 subtype3 
   14.99    17.03    17.13 
[1] "0.1 - 102.4 (15.0)" "0.1 - 139.2 (17.0)" "0.1 - 140.4 (17.1)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  68  28
  subtype2 106  52
  subtype3 104  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   28
  subtype2  106   52
  subtype3  104   16
        clus
vv       subtype1 subtype2 subtype3
  COLON        68      106      104
  RECTUM       28       52       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      13        0        5        29         1         0         1
  subtype2      18        0        9        42         2         2         5
  subtype3      21        1        6        38         4         1         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         13         11        6         7         0
  subtype2          9         28         13       12        12         0
  subtype3          2         15         10        8         6         1
D4V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          13       18       21
  STAGE IA          0        0        1
  STAGE II          5        9        6
  STAGE IIA        29       42       38
  STAGE IIB         1        2        4
  STAGE IIC         0        2        1
  STAGE III         1        5        5
  STAGE IIIA        7        9        2
  STAGE IIIB       13       28       15
  STAGE IIIC       11       13       10
  STAGE IV          6       12        8
  STAGE IVA         7       12        6
  STAGE IVB         0        0        1
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   3  11  68  15
  subtype2   5  22 114  17
  subtype3   3  22  80  14
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        5        3
  T2       11       22       22
  T3       68      114       80
  T4       15       17       14
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 52 28 17
  subtype2 80 48 27
  subtype3 74 24 22
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       52       80       74
  N1       28       48       24
  N2       17       27       22
[1] 3 3
[1] 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
  subtype1  70   9   2   0  14
  subtype2 105  19   5   0  28
  subtype3  85  10   2   1  19
D4V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        70      105       85
  M1         9       19       10
  M1A        2        5        2
  M1B        0        0        1
  MX        14       28       19
[1] 5 3
[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
  subtype1 38 60
  subtype2 68 90
  subtype3 64 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   60
  subtype2   68   90
  subtype3   64   56
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       68       64
  MALE         60       90       56
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   56                            12
  subtype2                  100                             6
  subtype3                   88                            16
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    27                              1
  subtype2                    49                              3
  subtype3                    14                              2
D4V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 56      100       88
  COLON MUCINOUS ADENOCARCINOMA        12        6       16
  RECTAL ADENOCARCINOMA                27       49       14
  RECTAL MUCINOUS ADENOCARCINOMA        1        3        2
[1] 4 3
[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
  subtype1   4  94
  subtype2   4 154
  subtype3   0 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   94
  subtype2    4  154
  subtype3    0  120
     clus
vv    subtype1 subtype2 subtype3
  NO         4        4        0
  YES       94      154      120
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  67   1   0   4
  subtype2 103   1   2  11
  subtype3  75   2   4  13
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       67      103       75
  R1        1        1        2
  R2        0        2        4
  RX        4       11       13
[1] 4 3
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        11
  subtype2                                0     4                        19
  subtype3                                0     4                        18
          vv
clus       WHITE
  subtype1    78
  subtype2   118
  subtype3    86
D4V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        4        4
  BLACK OR AFRICAN AMERICAN              11       19       18
  WHITE                                  78      118       86
[1] 4 3
[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 = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  73  19
  subtype2 129  39
  subtype3  37   5
  subtype4 113  24
subtype1 subtype2 subtype3 subtype4 
      92      168       42      137 
subtype1 subtype2 subtype3 subtype4 
      19       39        5       24 
$subtype1
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 
       37.02        17.79        35.11        37.25        16.04        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6782 
       29.16         8.38        25.08        24.16        21.76        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3655 TCGA-AA-3678 
        1.02        35.01         1.02        24.03        61.02        47.01 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3856 TCGA-AA-3864 
        0.99        35.05         0.99        38.99         0.99        53.00 
TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       17.03        33.01        21.99        16.08        50.99        34.06 
TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00K TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4308 
       27.02        18.05        18.05         0.20        17.82        75.25 
TCGA-AZ-4615 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6717 
       32.94         3.19         2.24         3.06         3.29         0.33 
TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        1.35         2.01         8.02        29.06        22.03        22.98 
TCGA-CM-5868 TCGA-CM-6167 TCGA-D5-5538 TCGA-D5-6922 TCGA-D5-6926 TCGA-DM-A28A 
       17.03        14.99        12.26        10.13         9.04        26.47 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6310 
        8.61        13.64         6.18         1.28         0.53        45.11 
TCGA-G4-6625 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3574 
       91.79        17.23        12.72        10.39        20.02        36.03 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 
        7.07         1.02         2.01        12.03        19.99         1.02 
TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A036 TCGA-DC-6156 
        0.99        36.03         1.02        17.03       117.11        15.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 
       12.95        10.06         5.29         9.96        14.86         0.66 
TCGA-F5-6863 TCGA-G5-6572 
        0.76        47.08 

$subtype2
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-5662 TCGA-A6-5664 
       46.65        23.38        42.28        15.52        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6652 
       22.06        32.71        27.09        22.52        20.61        24.69 
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       23.87         3.02         1.02        58.03        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3548 TCGA-AA-3555 
       38.99         9.07        19.07        34.03        33.99        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3688 TCGA-AA-3696 
       20.98        19.99        13.94        54.02        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3844 
       85.05        19.04         0.99        25.02        17.98        14.93 
TCGA-AA-3848 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00E 
        0.99         2.01        20.98        13.05         7.96        30.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01I 
       42.02        17.03        14.99        34.98        15.02        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E 
       35.01         1.02        35.01        26.01        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        39.98        40.96 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4682 
       56.55         1.58         0.20        21.44         5.65        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 
       65.00        61.41         6.77        29.56        11.74         1.94 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 TCGA-CK-6747 
        2.14         3.25         0.07         0.26        21.99         2.93 
TCGA-CM-4746 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6172 
       37.02        15.02        15.02        16.04        21.99        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       13.05        11.08        10.06        12.03        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6931 
       18.25         4.50        17.13        12.39        12.43        12.00 
TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6806 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       95.18        13.38        29.59        28.21         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-AF-2689 
       61.87        51.75        36.72        26.43        26.04        17.95 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 
        8.45        15.39        10.39         8.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03        34.03        50.04         6.05         0.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A00C 
       19.99         0.99         0.99         1.02        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       23.01        36.03         9.07        51.98         1.94        38.96 
TCGA-AH-6544 TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        0.49         4.60        10.98        12.99        13.97        36.00 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
        2.40        20.91        18.28        17.69        16.31         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 TCGA-G5-6641 
       10.78        13.64         0.39         1.02         1.12        26.43 

$subtype3
TCGA-A6-2681 TCGA-A6-6140 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 
       45.60        24.13        37.05         8.05        29.00        29.00 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3854 TCGA-AA-A004 TCGA-AA-A00F 
       13.02        24.00        19.99        36.03        13.94        34.03 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01P 
       17.03        21.99        15.02         0.99        32.02        38.07 
TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-5900 TCGA-AY-5543 
       33.04        51.98        14.01        41.00         0.07        15.75 
TCGA-CM-5863 TCGA-CM-6164 TCGA-D5-6531 TCGA-D5-6898 TCGA-D5-6924 TCGA-DM-A280 
       15.02        29.03        17.75         7.53        14.30         7.76 
TCGA-F4-6855 TCGA-G4-6323 TCGA-AG-3578 TCGA-AG-3891 TCGA-AG-4022 TCGA-AG-A011 
       35.41        13.78        32.02        18.02         0.99        37.02 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6549 TCGA-EI-6509 
       15.95         1.02        61.97        41.00         0.20        17.00 

$subtype4
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-5661 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       37.05        34.65        33.53        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
       19.66        17.95         0.92         5.98        26.99        33.04 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3862 TCGA-AA-3869 TCGA-AA-3950 TCGA-AA-3986 
       15.95        36.95        30.05        27.02        24.00        19.07 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A02R 
       38.04         4.01         0.99        31.00         1.02        22.03 
TCGA-AA-A03F TCGA-AD-6548 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4315 
       18.05        21.37         0.46         0.92        27.09        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
        1.41         5.13        49.41        12.10       100.01         5.23 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 
        0.10        21.14       124.27        23.05        20.02        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
        8.02        13.02        30.08        16.01        15.02         5.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       12.00        14.04        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        19.59        20.19        20.42 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
        1.32         7.92        15.12        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF 
       15.58         9.44        11.64         1.51        11.38        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A288 TCGA-F4-6461 
      130.65        92.75        12.59       135.65        14.04        11.11 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       13.45        35.87         1.55        16.31        16.24        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       19.43       107.67        23.51        74.56        43.07        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        39.42        35.93        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-AF-3914 
       35.80        26.17        46.75        47.15        52.80        37.68 
TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-A002 
       19.99        35.01        48.03        32.02        14.04        20.98 
TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AH-6547 
       25.97        31.00        70.03        64.01        10.98         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        0.69         0.72        10.19         7.99        11.01        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EI-6506 
        7.10        30.05        13.05        41.36        24.13        20.55 
TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6917 TCGA-F5-6465 
       19.96        15.85        16.34        16.41        17.46        37.51 
TCGA-F5-6571 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
       31.30         0.69         0.46        18.28        55.76 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  117.11   140.38    61.97   135.65 
subtype1 subtype2 subtype3 subtype4 
  17.130   18.265   19.005   19.660 
[1] "0.2 - 117.1 (17.1)" "0.1 - 140.4 (18.3)" "0.1 - 62.0 (19.0)" 
[4] "0.1 - 135.7 (19.7)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1  70  30
  subtype2 126  53
  subtype3  32  10
  subtype4 103  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70   30
  subtype2  126   53
  subtype3   32   10
  subtype4  103   37
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        70      126       32      103
  RECTUM       30       53       10       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        0        8        26         3         0         3
  subtype2      27        0       11        44         4         1        11
  subtype3       8        1        3        17         0         0         2
  subtype4      25        0        5        52         2         1         8
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         18         10       10         7         0
  subtype2          7         27         10       26         7         1
  subtype3          0          3          5        1         1         0
  subtype4          5         14         14        7         4         0
D5V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          10       27        8       25
  STAGE IA          0        0        1        0
  STAGE II          8       11        3        5
  STAGE IIA        26       44       17       52
  STAGE IIB         3        4        0        2
  STAGE IIC         0        1        0        1
  STAGE III         3       11        2        8
  STAGE IIIA        4        7        0        5
  STAGE IIIB       18       27        3       14
  STAGE IIIC       10       10        5       14
  STAGE IV         10       26        1        7
  STAGE IVA         7        7        1        4
  STAGE IVB         0        1        0        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   0  13  72  14
  subtype2   6  31 123  19
  subtype3   0   8  32   1
  subtype4   5  24  97  14
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        6        0        5
  T2       13       31        8       24
  T3       72      123       32       97
  T4       14       19        1       14
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 47 33 19
  subtype2 95 50 34
  subtype3 29  6  6
  subtype4 89 28 22
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       47       95       29       89
  N1       33       50        6       28
  N2       19       34        6       22
[1] 3 4
[1] 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
  subtype1  78  12   5   0   3
  subtype2 130  32   0   1  15
  subtype3  37   2   0   0   3
  subtype4 112   8   3   0  15
D5V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        78      130       37      112
  M1        12       32        2        8
  M1A        5        0        0        3
  M1B        0        1        0        0
  MX         3       15        3       15
[1] 5 4
[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
  subtype1 42 58
  subtype2 88 91
  subtype3 19 23
  subtype4 66 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   58
  subtype2   88   91
  subtype3   19   23
  subtype4   66   74
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       88       19       66
  MALE         58       91       23       74
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   61                             9
  subtype2                  119                             7
  subtype3                   27                             5
  subtype4                   86                            17
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    24                              4
  subtype2                    48                              4
  subtype3                     9                              1
  subtype4                    36                              1
D5V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 61      119       27       86
  COLON MUCINOUS ADENOCARCINOMA         9        7        5       17
  RECTAL ADENOCARCINOMA                24       48        9       36
  RECTAL MUCINOUS ADENOCARCINOMA        4        4        1        1
[1] 4 4
[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
  subtype1   3  97
  subtype2   3 176
  subtype3   0  42
  subtype4   2 138
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   97
  subtype2    3  176
  subtype3    0   42
  subtype4    2  138
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        3        0        2
  YES       97      176       42      138
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  74   0   7   7
  subtype2 114   1  18   6
  subtype3  38   0   1   1
  subtype4 112   1   2   5
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       74      114       38      112
  R1        0        1        0        1
  R2        7       18        1        2
  RX        7        6        1        5
[1] 4 4
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                         8
  subtype2                                0     5                         8
  subtype3                                0     0                         2
  subtype4                                1     1                         6
          vv
clus       WHITE
  subtype1    45
  subtype2    88
  subtype3    12
  subtype4   101
D5V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   6        5        0        1
  BLACK OR AFRICAN AMERICAN               8        8        2        6
  WHITE                                  45       88       12      101
[1] 4 4
[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 = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  45   8
  subtype2 223  65
  subtype3  84  14
subtype1 subtype2 subtype3 
      53      288       98 
subtype1 subtype2 subtype3 
       8       65       14 
$subtype1
TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5660 TCGA-A6-6142 
       37.02        37.05        37.25        33.34        29.19        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3812 TCGA-AA-3866 TCGA-AA-3950 
       24.16        21.76        20.28        35.05        17.03        24.00 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A02W TCGA-AD-5900 TCGA-AM-5820 TCGA-AY-6196 
       18.05        18.05        41.00         0.07         0.46         0.20 
TCGA-AZ-4308 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CM-4747 TCGA-CM-5868 TCGA-CM-6167 
       75.25         3.19         3.29         8.02        17.03        14.99 
TCGA-D5-5538 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-DM-A1D0 TCGA-F4-6459 
       12.26        10.13        14.30         9.04       130.65         8.61 
TCGA-F4-6463 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6310 
       13.64        16.31         1.28         0.53        43.07        45.11 
TCGA-G4-6314 TCGA-G4-6625 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3581 
       35.93        91.79        17.23        12.72        20.02         7.07 
TCGA-AG-A014 TCGA-AG-A036 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.95       117.11        15.02        12.95        10.06         5.29 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6863 TCGA-G5-6235 
        9.96        31.30        14.86         0.76        55.76 

$subtype2
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
       46.65        23.38        17.79        42.28        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
       15.52        16.04        32.75        36.53        32.91        30.44 
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-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       22.52        24.13         8.38        20.61        24.69        23.87 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02         3.02         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        38.99         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3548 
        8.05        19.07        34.03        29.00        29.00        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        24.00        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3681 
       19.99        61.02        54.02         0.92        47.01         5.98 
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-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
        0.99        33.04         0.99        25.02        17.98        38.99 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 
       14.93         0.99        36.03         0.99        53.00        27.02 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        33.01        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00E 
       13.05        34.06        27.02         7.96        13.94        30.02 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        17.03        42.02        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       34.98        15.02        15.02         0.99        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        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-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 
       14.01         0.92        22.03        39.98        40.96        56.55 
TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
        1.58         0.20        15.75        21.44        17.82        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94        22.36        65.00        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10        29.56        11.74         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-6719 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4748 
        1.35        21.99         2.93         2.01        37.02        26.04 
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-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       21.99        11.01        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       12.03        13.51        11.51        17.75        18.25         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6920 
       15.12        17.85         4.50        17.13         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.43        12.00        11.38       119.70        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-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-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6570 
       35.97        60.79        95.18        13.38        11.11         6.18 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.55        29.59        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 
       82.39        74.56        61.87        53.62        51.75        36.72 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 
       26.43        26.04        13.78        17.95        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 
       15.39        10.39        36.03        32.02         8.02         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-3609 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 
        0.99         1.02         0.99         0.99         1.02        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-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       23.01        37.02        36.03         9.07         1.02        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6549 
       51.98         1.94        38.96        61.97         0.49         0.20 
TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.60        10.98        15.02        12.99        13.97        36.00 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        0.49         2.40        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6810 
       16.31         8.61        10.78        13.64        17.46         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
        1.02         0.66         0.69         0.46        47.08        26.43 

$subtype3
TCGA-A6-3807 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       34.65        31.63        33.53        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3862 TCGA-AA-3986 
       19.66        17.95        15.95        36.95        30.05        19.07 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A03F 
       38.04         4.01         0.99        31.00         1.02        18.05 
TCGA-AD-6548 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6601 
       21.37         0.92        27.09         1.41         5.13       100.01 
TCGA-AZ-6605 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        5.23         0.10        21.14       124.27        23.05        20.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6169 
        8.02        13.02         5.03        14.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6529 
       15.02        14.04        12.95        11.01        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 
       20.42         1.32        12.49        16.14        15.58         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6569 TCGA-F4-6703 
       11.64         1.51        38.20       135.65        13.45        35.87 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6298 TCGA-G4-6306 TCGA-G4-6307 
       16.24        33.67        19.43        23.51        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       39.42        36.00        22.09        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-AF-3914 TCGA-AG-3882 TCGA-AG-3891 TCGA-AG-3893 
       47.15        52.80        37.68        19.99        18.02        35.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01W 
       48.03        32.02        14.04        25.97        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       64.01        41.00         1.45         0.69         0.72        10.19 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DC 
        7.99        11.01         7.10        30.05        13.05        41.36 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6465 
       20.55        19.96        15.85        16.34        16.41        37.51 
TCGA-F5-6861 TCGA-G5-6233 
        1.12        18.28 

subtype1 subtype2 subtype3 
    0.07     0.07     0.10 
subtype1 subtype2 subtype3 
  130.65   140.38   135.65 
subtype1 subtype2 subtype3 
  17.030   18.115   19.810 
[1] "0.1 - 130.7 (17.0)" "0.1 - 140.4 (18.1)" "0.1 - 135.7 (19.8)"
D6V2, continuous
D6V3, binary
          cls
clus         0   1
  subtype1  39  15
  subtype2 223  84
  subtype3  69  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   15
  subtype2  223   84
  subtype3   69   31
        clus
vv       subtype1 subtype2 subtype3
  COLON        39      223       69
  RECTUM       15       84       31
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       6        0        1        15         1         0         1
  subtype2      40        1       22        90         7         1        19
  subtype3      24        0        4        34         1         1         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         10          5        4         8         0
  subtype2          8         41         27       36         8         1
  subtype3          5         11          7        4         3         0
D6V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           6       40       24
  STAGE IA          0        1        0
  STAGE II          1       22        4
  STAGE IIA        15       90       34
  STAGE IIB         1        7        1
  STAGE IIC         0        1        1
  STAGE III         1       19        4
  STAGE IIIA        3        8        5
  STAGE IIIB       10       41       11
  STAGE IIIC        5       27        7
  STAGE IV          4       36        4
  STAGE IVA         8        8        3
  STAGE IVB         0        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   0   7  36  11
  subtype2   7  45 223  30
  subtype3   4  24  65   7
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        7        4
  T2        7       45       24
  T3       36      223       65
  T4       11       30        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  23  17  14
  subtype2 168  82  55
  subtype3  69  18  12
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       23      168       69
  N1       17       82       18
  N2       14       55       12
[1] 3 3
[1] 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
  subtype1  37   7   5   0   4
  subtype2 239  43   0   1  21
  subtype3  81   4   3   0  11
D6V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        37      239       81
  M1         7       43        4
  M1A        5        0        3
  M1B        0        1        0
  MX         4       21       11
[1] 5 3
[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
  subtype1  26  28
  subtype2 149 158
  subtype3  40  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   28
  subtype2  149  158
  subtype3   40   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26      149       40
  MALE         28      158       60
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   33                             6
  subtype2                  202                            21
  subtype3                   58                            11
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    13                              2
  subtype2                    73                              8
  subtype3                    31                              0
D6V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 33      202       58
  COLON MUCINOUS ADENOCARCINOMA         6       21       11
  RECTAL ADENOCARCINOMA                13       73       31
  RECTAL MUCINOUS ADENOCARCINOMA        2        8        0
[1] 4 3
[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
  subtype1   3  51
  subtype2   3 304
  subtype3   2  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    3  304
  subtype3    2   98
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        2
  YES       51      304       98
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  44   1   1   1
  subtype2 212   1  26  14
  subtype3  82   0   1   4
D6V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       44      212       82
  R1        1        1        0
  R2        1       26        1
  RX        1       14        4
[1] 4 3
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         3
  subtype2                                1     9                        15
  subtype3                                0     1                         6
          vv
clus       WHITE
  subtype1    39
  subtype2   137
  subtype3    70
D6V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   2        9        1
  BLACK OR AFRICAN AMERICAN               3       15        6
  WHITE                                  39      137       70
[1] 4 3
[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 = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 101  33
  subtype2  98  29
  subtype3 107  20
  subtype4 157  27
subtype1 subtype2 subtype3 subtype4 
     134      127      127      184 
subtype1 subtype2 subtype3 subtype4 
      33       29       20       27 
$subtype1
TCGA-3L-AA1B TCGA-A6-2677 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
        5.06        17.79        32.91        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       32.71        29.16        24.13        25.18        20.61        24.69 
TCGA-A6-A567 TCGA-AA-3494 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3526 
       61.84         1.02        62.96         6.97        38.99        19.07 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3955 TCGA-AA-A01X 
       29.00        26.01        78.08        85.05        20.98        26.01 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 
       39.98         5.03        14.01        41.00         4.21         0.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AZ-4682 TCGA-AZ-5403 
        0.10         0.20         0.43        14.50        22.36        62.79 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       29.56         1.94         2.14         3.29         0.07         0.26 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       48.20        21.99        22.03         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6676 
       15.02        14.04        29.03        21.99        15.02        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 
       11.01        14.99        13.51        18.25         1.32         4.50 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       17.13        14.30        13.41        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       12.59       140.38        44.32       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 
       81.37       119.93        35.97        60.79       117.07        13.38 
TCGA-F4-6808 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       33.67         0.53        28.21        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL 
       36.00        46.75         4.11        10.98        26.99        30.28 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3742 TCGA-AG-4022 TCGA-AG-A01N 
       37.74         8.45        36.03         0.99         0.99        31.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6549 TCGA-AH-6897 TCGA-CI-6622 TCGA-CI-6623 
        1.94        38.96         0.20         4.60         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-6681 
       15.02        12.99        12.00        13.97        36.00        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       13.05        10.06       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       32.61         0.49        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6810 TCGA-F5-6861 TCGA-F5-6863 
       16.31        11.51        11.97         0.39         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

$subtype2
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       43.76        43.43        13.94        37.05        37.25        16.04 
TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       33.34        31.63        22.09        22.52        25.08        21.76 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       23.87        19.66        20.28        24.92        52.44         9.63 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3870 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6548 
        1.02         1.02        29.98        38.07         0.07        21.37 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.58         1.02         0.76         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6601 
       27.09         0.20         1.41        32.94         5.13       100.01 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        5.23         3.19         0.33         0.10         1.35       102.44 
TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5349 
       70.16        21.14         2.01         8.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       16.01        12.00        16.04        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 
       12.95        11.08        10.06        12.26        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.75         7.92        17.85        15.58         7.53        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-A0XD TCGA-DM-A1HA TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       10.26        24.43       131.51         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
        1.28        35.41         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6627 
       43.07        61.87        39.42        35.93        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z1 TCGA-AF-2687 
       52.80        10.52         2.79         5.98         6.64        24.13 
TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3731 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       17.23        20.02         1.02         0.69         0.72        10.19 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 
       15.02         7.10         5.29       129.27        24.13         2.40 
TCGA-EI-6507 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       19.96        13.64        17.46         8.45         9.96        37.51 
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-F5-6864 
        0.46 

$subtype3
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6649 
       14.53        33.53        22.06        27.09         8.38        24.16 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-A565 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       24.39        20.12        16.24         3.02        37.05        35.01 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3655 
       58.03        13.02        37.05         8.05        23.01        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        6.05         6.97        54.02        11.01         5.98        37.05 
TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3862 
       19.04        15.95        33.07        36.03        32.05        30.05 
TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02Y TCGA-AA-A03F 
       53.00         4.01        37.02        39.06        39.98        18.05 
TCGA-AD-6889 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       56.55        15.75        21.44        17.82         5.19         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
       50.37        58.39         5.65        65.00        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        6.77        12.10        11.74         2.24         3.06         3.25 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 
       17.56        40.34        15.62        51.32         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 
       23.05        20.02        37.02        27.02        15.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 
       14.04        11.01        13.05        12.03        19.59        20.42 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 
       15.12        12.49        16.14        12.39        12.00       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 
       92.75        49.91         7.50       135.65         7.76        14.04 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 
       98.24        95.18        29.59        19.43       107.67        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       44.68        51.75        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2693 
       35.80        26.17         5.59        17.29        14.76        19.10 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3599 
       14.50        15.39        10.39        32.02         2.01        12.03 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A008 TCGA-AG-A02N TCGA-AH-6544 
       32.98        13.02        32.02        13.94        61.97         0.49 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-6160 TCGA-EI-6506 
        1.45         1.81         6.05         6.05        30.05        20.55 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-G5-6233 
       18.28        17.69        16.41         8.61        10.78        18.28 
TCGA-G5-6641 
       26.43 

$subtype4
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        23.38        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       45.60        15.52        34.65        32.75        36.53        32.45 
TCGA-AA-3488 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        5.03         1.02         1.02         9.07        24.03        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       19.99        13.94        19.99         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       50.04        47.01        15.02        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99         0.99         0.99        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02         1.02        17.98        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       14.93        17.03         0.99         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 
       34.03         2.01        21.99        36.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
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-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       35.01        51.98         2.96         2.01         0.92        22.03 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4748 
       40.96        16.31         0.95        75.25        83.80        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
        8.02        13.02        29.06        43.04        13.55        12.72 
TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       10.39        12.00         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-3600 
       24.00         1.02        46.03        34.03        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       29.98         0.99        19.99         1.02        36.95        17.03 
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-A002 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97        41.00        38.04       117.11 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.49     0.92 
subtype1 subtype2 subtype3 subtype4 
  140.38   131.51   135.65   117.11 
subtype1 subtype2 subtype3 subtype4 
  17.080   13.640   19.040   20.485 
[1] "0.1 - 140.4 (17.1)" "0.1 - 131.5 (13.6)" "0.5 - 135.7 (19.0)"
[4] "0.9 - 117.1 (20.5)"
D7V2, continuous
D7V3, binary
          cls
clus         0   1
  subtype1  93  46
  subtype2 103  28
  subtype3 106  27
  subtype4 135  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93   46
  subtype2  103   28
  subtype3  106   27
  subtype4  135   59
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        93      103      106      135
  RECTUM       46       28       27       59
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      24        0        7        31         2         2         4
  subtype2      12        0        5        44         2         0         2
  subtype3      28        1       10        42         2         1         8
  subtype4      38        0       13        54         5         0        13
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          5         23         10       13        11         0
  subtype2          5         18         18       14         7         0
  subtype3          6         15          5        7         7         1
  subtype4          5         22         19       25         1         0
D7V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          24       12       28       38
  STAGE IA          0        0        1        0
  STAGE II          7        5       10       13
  STAGE IIA        31       44       42       54
  STAGE IIB         2        2        2        5
  STAGE IIC         2        0        1        0
  STAGE III         4        2        8       13
  STAGE IIIA        5        5        6        5
  STAGE IIIB       23       18       15       22
  STAGE IIIC       10       18        5       19
  STAGE IV         13       14        7       25
  STAGE IVA        11        7        7        1
  STAGE IVB         0        0        1        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   6  28  89  15
  subtype2   1  13  95  22
  subtype3   4  28  90  12
  subtype4   9  36 135  16
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        6        1        4        9
  T2       28       13       28       36
  T3       89       95       90      135
  T4       15       22       12       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  78  38  20
  subtype2  64  34  32
  subtype3  87  30  18
  subtype4 112  45  39
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       78       64       87      112
  N1       38       34       30       45
  N2       20       32       18       39
[1] 3 4
[1] 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
  subtype1  91  18   6   0  22
  subtype2  91  17   3   0  17
  subtype3 100  11   0   1  22
  subtype4 167  25   1   0   0
D7V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        91       91      100      167
  M1        18       17       11       25
  M1A        6        3        0        1
  M1B        0        0        1        0
  MX        22       17       22        0
[1] 5 4
[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
  subtype1 63 76
  subtype2 55 76
  subtype3 62 73
  subtype4 99 97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   76
  subtype2   55   76
  subtype3   62   73
  subtype4   99   97
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       63       55       62       99
  MALE         76       76       73       97
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   90                             3
  subtype2                   86                            17
  subtype3                   85                            20
  subtype4                  118                            17
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    46                              0
  subtype2                    25                              3
  subtype3                    20                              6
  subtype4                    53                              4
D7V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 90       86       85      118
  COLON MUCINOUS ADENOCARCINOMA         3       17       20       17
  RECTAL ADENOCARCINOMA                46       25       20       53
  RECTAL MUCINOUS ADENOCARCINOMA        0        3        6        4
[1] 4 4
[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
  subtype1   2 137
  subtype2   3 128
  subtype3   3 132
  subtype4   1 195
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  137
  subtype2    3  128
  subtype3    3  132
  subtype4    1  195
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        3        3        1
  YES      137      128      132      195
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  79   2   7  10
  subtype2  96   1   3   9
  subtype3  91   1   3   9
  subtype4 168   1  22   0
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       79       96       91      168
  R1        2        1        1        1
  R2        7        3        3       22
  RX       10        9        9        0
[1] 4 4
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        12
  subtype2                                1     4                        14
  subtype3                                0     4                        17
  subtype4                                0     0                         4
          vv
clus       WHITE
  subtype1    98
  subtype2   104
  subtype3    72
  subtype4    20
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   4        4        4        0
  BLACK OR AFRICAN AMERICAN              12       14       17        4
  WHITE                                  98      104       72       20
[1] 4 4
[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 = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  57  20
  subtype2 100  16
  subtype3  75  21
  subtype4  47  14
  subtype5 118  23
  subtype6  29   5
  subtype7  37  10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      77      116       96       61      141       34       47 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      20       16       21       14       23        5       10 
$subtype1
TCGA-3L-AA1B TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6650 
        5.06        32.91        29.19        22.09        32.71        20.61 
TCGA-A6-6652 TCGA-A6-A5ZU TCGA-AA-A02K TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       24.69         9.63        14.01         0.20         0.43        14.50 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 
        1.94         2.14         0.07         0.26       102.44        48.20 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6677 TCGA-CM-6678 
        5.03        15.02        15.02        21.99        11.08        11.01 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       14.99        12.26        13.51        17.75        18.25         1.32 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
        4.50        17.13        13.41        11.38        38.20       130.65 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38        44.32       131.51       139.17         6.12 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 
       26.47        81.37       119.93        60.79       117.07        13.64 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6626 
       35.41        28.21        23.51        55.04        36.00        46.75 
TCGA-NH-A50T TCGA-RU-A8FL TCGA-AF-5654 TCGA-AG-3742 TCGA-AG-A002 TCGA-AH-6549 
        4.11        30.28         8.45         0.99        20.98         0.20 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
        0.69         4.60         7.99        11.01        12.99        12.00 
TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       36.00       126.44        41.36        51.48        32.61         0.49 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-F5-6811 TCGA-F5-6861 
       17.00        15.85        16.34         1.02         1.12 

$subtype2
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       13.94        14.53        27.09        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6780 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3495 TCGA-AA-3496 
       24.16        20.12        16.24        24.92        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3526 TCGA-AA-3655 
       35.01        58.03        62.96         6.97        19.07        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A01Z 
       78.08         6.05        37.05        85.05        19.04        37.02 
TCGA-AA-A02Y TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AY-5543 
       39.98        21.37         4.21         0.79         0.10        15.75 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         5.19         5.52        58.39        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 
        6.77        12.10        11.74         3.25        17.56        40.34 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5863 
       21.99         2.93       124.27        27.02        16.01        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6529 
       12.00        14.04        11.01        12.03        19.59        20.19 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 
       15.12        12.49        15.58        12.39        12.00       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M 
       92.75        13.32         7.76        14.04        35.97        95.18 
TCGA-F4-6461 TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6304 
       11.11        29.59        33.67       107.67         8.35        53.62 
TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       44.68        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YV 
       91.79        10.98        10.52         2.79         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       17.29        14.76        19.10        14.50        15.39        10.39 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3902 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 
        1.02        32.98        32.02         0.49         1.45         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-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6508 
       10.98        15.02        13.97        30.05        20.55        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7004 TCGA-G5-6233 
       18.28        17.69        16.41        10.78         8.45        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype3
TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       43.43        37.05        37.25        31.63        30.44        23.61 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 
       29.16        22.52        25.08        21.76        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-A01X TCGA-AD-6899 TCGA-AD-6901 
       61.84        52.44         1.02        26.01         1.58         1.02 
TCGA-AM-5820 TCGA-AZ-4323 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        0.46         1.41        65.00        62.79        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
        3.19         3.29         0.33         1.35         2.01         8.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6165 
       22.03        22.98        30.08        17.03        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 
       14.99        12.99        13.02        15.02        11.08        10.06 
TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       11.51         7.92         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
        9.04         8.61        13.38         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 
        1.28         0.53        82.39        43.07        61.87        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6627 TCGA-QG-A5Z1 TCGA-AF-2687 TCGA-AF-2690 
       39.42        35.93        47.15         6.64        24.13        17.23 
TCGA-AF-3911 TCGA-AF-6655 TCGA-AG-4022 TCGA-AH-6644 TCGA-CL-5917 TCGA-DC-6156 
       37.74        20.02         0.99         0.72        60.03        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD 
        7.10        12.95        13.05        10.06         5.29        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 
      129.27        24.13         2.40        16.31        11.51        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.66         0.69         0.53         0.76         0.46        47.08 

$subtype4
TCGA-A6-2686 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 
       16.04        33.53        22.06        24.39        19.66         3.02 
TCGA-AA-3663 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
        6.97        38.07         0.07        56.55         0.72         0.76 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4313 TCGA-AZ-4614 
        0.92        27.09         0.20        21.44        50.37         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 
       32.94         5.13        49.41       100.01         2.24         3.06 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
        0.10        70.16        15.62        51.32        21.14        23.05 
TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 
       20.02        15.02        14.04        12.95        13.05        20.42 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       17.85        16.14         9.44        11.64         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 
       24.43        49.91         7.50       135.65        98.24        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6586 
        6.18        35.87        19.43        74.56        51.75        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A6GA TCGA-BM-6198 TCGA-EI-6507 TCGA-EI-6882 
       26.17        52.80         5.98        10.19        19.96         8.61 
TCGA-EI-6917 
       17.46 

$subtype5
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       37.02        17.79        44.91        35.11        45.60        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3514 TCGA-AA-3517 
       34.65        36.53         5.03         1.02         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        9.07        36.03        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 
       26.01        12.99        14.01        21.01        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 
       19.99         2.01        14.01        47.01        15.02        19.00 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       35.05        25.02        17.98        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        32.05         0.99        31.07        31.07 
TCGA-AA-3862 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
       30.05        17.03        24.03        27.02        18.05        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 
        2.01        20.98        34.03        21.99        36.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       19.07         7.96        13.94        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-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-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
       15.02         0.99        32.02        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       33.04         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4748 
       40.96        16.31         0.95        75.25        83.80        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AF-2692 TCGA-AF-3913 TCGA-AG-3574 
        8.02        13.02        29.06        13.55        10.39        36.03 
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-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       46.03        34.03        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98         0.99        19.99         1.02        17.03 
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-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        64.01        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 
       38.96        38.04       117.11 

$subtype6
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3516 
       46.65        43.76        23.38        33.34        32.75        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3664 
        1.02         8.05         0.99        17.95        29.95        54.02 
TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
        0.92         5.98        26.99         0.99         0.99        33.04 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
        1.02        15.95        29.98        31.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A01R 
       24.00         2.01        30.02        18.05         0.99        35.01 
TCGA-AA-A02R TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3600 
       22.03        12.72        12.00         6.05 

$subtype7
TCGA-A6-2678 TCGA-A6-4107 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3548 TCGA-AA-3552 
       42.28        32.45        24.03        37.05        33.99        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 
       23.01        19.99        50.04        11.01        36.00         5.03 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3930 
        0.99        38.99        33.07        36.03        53.00         2.01 
TCGA-AA-3939 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00N 
       12.99        25.02        27.02        27.02        38.04         4.01 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01Q TCGA-AA-A01V TCGA-AA-A024 
       17.03        34.98        12.00         1.02        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A03F TCGA-CM-4746 TCGA-AF-2691 TCGA-AG-3578 
       51.98         0.92        18.05        37.02        43.04        32.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3892 
        2.01        50.04        12.03         0.99        36.95        13.02 
TCGA-AG-A008 TCGA-AG-A015 TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
       13.94        36.03        10.98        61.97        41.00 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.10     0.33     0.07     0.95     0.92     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  140.38   124.27   129.27   135.65   117.11    54.02    61.97 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  15.850   16.325   14.925   17.850   19.990   20.040   27.020 
[1] "0.1 - 140.4 (15.8)" "0.1 - 124.3 (16.3)" "0.3 - 129.3 (14.9)"
[4] "0.1 - 135.7 (17.9)" "0.9 - 117.1 (20.0)" "0.9 - 54.0 (20.0)" 
[7] "0.9 - 62.0 (27.0)" 
D8V2, continuous
D8V3, binary
          cls
clus         0   1
  subtype1  57  22
  subtype2  87  32
  subtype3  64  32
  subtype4  59   4
  subtype5 100  51
  subtype6  34   5
  subtype7  36  14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   22
  subtype2   87   32
  subtype3   64   32
  subtype4   59    4
  subtype5  100   51
  subtype6   34    5
  subtype7   36   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COLON        57       87       64       59      100       34       36
  RECTUM       22       32       32        4       51        5       14
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      14        0        0        25         1         1         0
  subtype2      20        1        8        25         2         1         7
  subtype3       8        0        4        26         1         1         2
  subtype4      13        0        4        28         1         0         2
  subtype5      32        0        7        39         1         0         9
  subtype6       4        0        4        14         3         0         5
  subtype7      11        0        8        14         2         0         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         12          9        5         5         0
  subtype2          8         21          6        9         9         0
  subtype3          3         16         12        9        10         0
  subtype4          1          4          5        1         1         1
  subtype5          5         16         16       27         1         0
  subtype6          0          5          1        3         0         0
  subtype7          0          4          3        5         0         0
D8V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          14       20        8       13       32        4       11
  STAGE IA          0        1        0        0        0        0        0
  STAGE II          0        8        4        4        7        4        8
  STAGE IIA        25       25       26       28       39       14       14
  STAGE IIB         1        2        1        1        1        3        2
  STAGE IIC         1        1        1        0        0        0        0
  STAGE III         0        7        2        2        9        5        2
  STAGE IIIA        4        8        3        1        5        0        0
  STAGE IIIB       12       21       16        4       16        5        4
  STAGE IIIC        9        6       12        5       16        1        3
  STAGE IV          5        9        9        1       27        3        5
  STAGE IVA         5        9       10        1        1        0        0
  STAGE IVB         0        0        0        1        0        0        0
[1] 13  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   1  15  54   9
  subtype2   7  20  77  16
  subtype3   0  12  70  13
  subtype4   2  11  44   6
  subtype5   6  35 100  12
  subtype6   1   3  29   6
  subtype7   3   9  35   3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        1        7        0        2        6        1        3
  T2       15       20       12       11       35        3        9
  T3       54       77       70       44      100       29       35
  T4        9       16       13        6       12        6        3
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 44 18 16
  subtype2 66 39 15
  subtype3 41 30 23
  subtype4 46  9  8
  subtype5 83 37 33
  subtype6 25  7  7
  subtype7 36  7  7
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       44       66       41       46       83       25       36
  N1       18       39       30        9       37        7        7
  N2       16       15       23        8       33        7        7
[1] 3 7
[1] 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
  subtype1  55   8   2   0  13
  subtype2  81  12   2   0  26
  subtype3  62  14   5   0  14
  subtype4  48   2   0   1   8
  subtype5 123  27   1   0   0
  subtype6  36   3   0   0   0
  subtype7  44   5   0   0   0
D8V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0        55       81       62       48      123       36       44
  M1         8       12       14        2       27        3        5
  M1A        2        2        5        0        1        0        0
  M1B        0        0        0        1        0        0        0
  MX        13       26       14        8        0        0        0
[1] 5 7
[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
  subtype1 36 43
  subtype2 53 68
  subtype3 43 53
  subtype4 26 37
  subtype5 72 81
  subtype6 27 12
  subtype7 22 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   43
  subtype2   53   68
  subtype3   43   53
  subtype4   26   37
  subtype5   72   81
  subtype6   27   12
  subtype7   22   28
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       36       53       43       26       72       27       22
  MALE         43       68       53       37       81       12       28
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   54                             3
  subtype2                   75                            12
  subtype3                   58                             6
  subtype4                   47                            12
  subtype5                   98                             2
  subtype6                   21                            13
  subtype7                   26                             9
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    22                              0
  subtype2                    29                              3
  subtype3                    31                              1
  subtype4                     3                              1
  subtype5                    49                              1
  subtype6                     2                              2
  subtype7                     8                              5
D8V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 54       75       58       47       98
  COLON MUCINOUS ADENOCARCINOMA         3       12        6       12        2
  RECTAL ADENOCARCINOMA                22       29       31        3       49
  RECTAL MUCINOUS ADENOCARCINOMA        0        3        1        1        1
                                clus
vv                               subtype6 subtype7
  COLON ADENOCARCINOMA                 21       26
  COLON MUCINOUS ADENOCARCINOMA        13        9
  RECTAL ADENOCARCINOMA                 2        8
  RECTAL MUCINOUS ADENOCARCINOMA        2        5
[1] 4 7
[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
  subtype1   0  79
  subtype2   2 119
  subtype3   5  91
  subtype4   1  62
  subtype5   0 153
  subtype6   1  38
  subtype7   0  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   79
  subtype2    2  119
  subtype3    5   91
  subtype4    1   62
  subtype5    0  153
  subtype6    1   38
  subtype7    0   50
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        2        5        1        0        1        0
  YES       79      119       91       62      153       38       50
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  43   0   2   8
  subtype2  77   2   3   6
  subtype3  69   0   0   6
  subtype4  41   1   0   8
  subtype5 126   2  24   0
  subtype6  35   0   1   0
  subtype7  43   0   5   0
D8V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       43       77       69       41      126       35       43
  R1        0        2        0        1        2        0        0
  R2        2        3        0        0       24        1        5
  RX        8        6        6        8        0        0        0
[1] 4 7
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        12
  subtype2                                0     1                        17
  subtype3                                1     4                         8
  subtype4                                0     4                         5
  subtype5                                0     0                         4
  subtype6                                0     0                         0
  subtype7                                0     0                         1
          vv
clus       WHITE
  subtype1    60
  subtype2    80
  subtype3    80
  subtype4    51
  subtype5    14
  subtype6     6
  subtype7     3
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   3        1        4        4        0
  BLACK OR AFRICAN AMERICAN              12       17        8        5        4
  WHITE                                  60       80       80       51       14
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        0
  BLACK OR AFRICAN AMERICAN               0        1
  WHITE                                   6        3
[1] 4 7
[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 = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 165  40
  subtype2  73  22
  subtype3 180  40
subtype1 subtype2 subtype3 
     205       95      220 
subtype1 subtype2 subtype3 
      40       22       40 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       43.43        14.53        32.91        30.44        29.19        33.53 
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-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3511 
       25.08        25.18        20.61        20.28         1.02         6.97 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 
       61.02        78.08         6.05         6.97        85.05        19.04 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       39.98         2.01        21.37         4.21        56.55         0.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6197 
        0.10         0.20         0.92        14.50        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       17.82         5.13        61.41        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         1.94         2.24         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.26         1.35        17.56       102.44        40.34        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.99         2.93       124.27        23.05 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       27.02        22.03        30.08        16.01         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 
       17.03        15.02        14.04        29.03        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        14.99        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       20.19        17.75        18.25         1.32        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14        15.58        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30        13.41        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        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-F4-6570 TCGA-F4-6806 TCGA-F4-6808 
      117.07        98.24        95.18         6.18        29.59        33.67 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        36.72        36.00        26.43        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-5654 
       35.80        91.79        46.75        52.80        19.10         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-4001 
       15.39        20.02        10.39        32.98         0.99        36.03 
TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
        0.99         0.49         0.20         0.69        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-6155 
        7.99        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00         7.10        30.05        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-F5-6465 
       18.28        15.85        17.69        16.34        16.31        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       31.30         0.39         1.02        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$subtype2
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 
       37.02        45.60        37.05        37.25        33.34        31.63 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       23.61        22.09         8.38        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3818 TCGA-AA-3994 TCGA-AA-A00O 
       23.87        19.66         1.02         0.99        27.02        27.02 
TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6899 
       38.07        26.01         2.96         0.07         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4308 
        1.02         0.76         0.46        27.09         0.20        75.25 
TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        1.41        62.79       100.01        29.56         5.23         3.19 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4747 
        3.06         0.33         0.10        21.14         2.01         8.02 
TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6165 
       26.04        22.98        15.02        15.02        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 
       14.99        12.99        12.95        10.06        19.59         7.92 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       17.85         7.53        10.13         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A1D6 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
        1.51        10.26        49.91         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.64        13.45        35.87         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6310 TCGA-G4-6314 
        1.28         0.53        19.43        43.07        45.11        35.93 
TCGA-G4-6321 TCGA-G4-6627 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 
       22.09        47.15        24.13        17.23        37.74        14.50 
TCGA-AG-3575 TCGA-AG-3731 TCGA-AG-A015 TCGA-AH-6547 TCGA-AH-6644 TCGA-DC-6681 
       12.00         1.02        36.03         1.45         0.72        12.95 
TCGA-DT-5265 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        5.29         9.96        14.86         0.66         0.69 

$subtype3
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-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       35.11        13.94        15.52        16.04        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3488 TCGA-AA-3492 
       36.53        32.45        24.39        20.12         5.03         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 
        1.02        37.05        35.01        58.03        62.96        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-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99         0.99         0.99        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-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-3862 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        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-3970 TCGA-AA-3971 
       20.98        34.03         2.01        21.99        36.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00J 
       27.02        27.02        19.07         7.96        19.00        18.05 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D 
       17.03        42.02        17.03        14.99        34.98         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       32.02        12.00        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       37.02        39.06        51.98         5.03        14.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       22.03        39.98        18.05        40.96        16.31         0.95 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       50.37        58.39         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4750 
       65.00         2.14        70.16        20.02        37.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-D5-6530 TCGA-D5-6931 TCGA-G4-6588 TCGA-AF-2689 
       13.02        29.06        20.42        12.00        26.17        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3578 
       43.04        13.55        12.72        10.39        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-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       29.98         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-A002 
       19.99        28.04        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
       13.94         6.02        37.02         9.07        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-EI-6507 
       61.97        41.00       117.11        19.96 

subtype1 subtype2 subtype3 
    0.07     0.07     0.92 
subtype1 subtype2 subtype3 
  140.38   100.01   117.11 
subtype1 subtype2 subtype3 
  17.820   13.640   20.995 
[1] "0.1 - 140.4 (17.8)" "0.1 - 100.0 (13.6)" "0.9 - 117.1 (21.0)"
D9V2, continuous
D9V3, binary
          cls
clus         0   1
  subtype1 150  61
  subtype2  80  15
  subtype3 175  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  150   61
  subtype2   80   15
  subtype3  175   64
        clus
vv       subtype1 subtype2 subtype3
  COLON       150       80      175
  RECTUM       61       15       64
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      32        1        8        67         4         2         8
  subtype2       9        0        5        26         0         0         3
  subtype3      53        0       23        61         6         0        16
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          9         33         13       16        11         1
  subtype2          3         15         14        7         8         0
  subtype3          4         21         18       34         4         0
D9V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          32        9       53
  STAGE IA          1        0        0
  STAGE II          8        5       23
  STAGE IIA        67       26       61
  STAGE IIB         4        0        6
  STAGE IIC         2        0        0
  STAGE III         8        3       16
  STAGE IIIA        9        3        4
  STAGE IIIB       33       15       21
  STAGE IIIC       13       14       18
  STAGE IV         16        7       34
  STAGE IVA        11        8        4
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   8  33 151  18
  subtype2   2  10  69  15
  subtype3  10  52 156  23
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        2       10
  T2       33       10       52
  T3      151       69      156
  T4       18       15       23
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 121  58  30
  subtype2  43  29  23
  subtype3 149  46  46
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      121       43      149
  N1       58       29       46
  N2       30       23       46
[1] 3 3
[1] 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
  subtype1 149  19   6   1  33
  subtype2  65  12   2   0  15
  subtype3 198  37   1   0   2
D9V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       149       65      198
  M1        19       12       37
  M1A        6        2        1
  M1B        1        0        0
  MX        33       15        2
[1] 5 3
[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
  subtype1 102 110
  subtype2  40  56
  subtype3 115 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102  110
  subtype2   40   56
  subtype3  115  126
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      102       40      115
  MALE        110       56      126
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  140                            10
  subtype2                   61                            19
  subtype3                  150                            24
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    60                              1
  subtype2                    13                              2
  subtype3                    54                              7
D9V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                140       61      150
  COLON MUCINOUS ADENOCARCINOMA        10       19       24
  RECTAL ADENOCARCINOMA                60       13       54
  RECTAL MUCINOUS ADENOCARCINOMA        1        2        7
[1] 4 3
[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
  subtype1   3 209
  subtype2   4  92
  subtype3   2 239
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  209
  subtype2    4   92
  subtype3    2  239
     clus
vv    subtype1 subtype2 subtype3
  NO         3        4        2
  YES      209       92      239
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 121   2   5  17
  subtype2  66   0   2   7
  subtype3 197   3  29   2
D9V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      121       66      197
  R1        2        0        3
  R2        5        2       29
  RX       17        7        2
[1] 4 3
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        14
  subtype2                                1     4                         7
  subtype3                                0     1                         5
          vv
clus       WHITE
  subtype1   171
  subtype2    73
  subtype3    36
D9V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   7        4        1
  BLACK OR AFRICAN AMERICAN              14        7        5
  WHITE                                 171       73       36
[1] 4 3
[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 = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 175  48
  subtype2 110  25
  subtype3 133  29
subtype1 subtype2 subtype3 
     223      135      162 
subtype1 subtype2 subtype3 
      48       25       29 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       43.43        14.53        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.06        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-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        19.66        20.28         1.02        35.01         6.97 
TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 
        1.02        61.02        78.08         6.97        85.05        19.04 
TCGA-AA-A010 TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       34.98         2.96         2.01         0.07         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AM-5820 
        0.79         0.72         1.58         1.02         0.10         0.46 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        15.75         0.20        21.44        17.82 
TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        62.79        61.41        49.41        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-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        48.20        51.32        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 
        2.01       124.27        23.05        27.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       16.01        15.02        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       14.04        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 
       11.01        10.06        12.03        14.99        19.59        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-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.50        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-A1D4 TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K 
        7.76        14.04        26.47        81.37       119.93        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18         8.61        11.11        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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        82.39        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-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       39.42        36.00        26.43        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-AF-2690 
       26.17        91.79        46.75        47.15        52.80        17.23 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       19.10        37.74        14.50        15.39        20.02        10.39 
TCGA-AG-3594 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3892 TCGA-AG-4022 
        2.01         7.99        32.98         0.99        13.02         0.99 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 
        0.49         1.45         0.72        10.19         6.97         9.37 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        7.99        10.98        11.01        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-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6509 
       41.36        24.13        51.48        32.61         2.40        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 
       18.28        15.85        17.69        16.31         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6235 
       31.30         1.02         0.66         0.69        18.28        55.76 
TCGA-G5-6572 
       47.08 

$subtype2
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-3809 TCGA-A6-5660 
       43.76        17.79        42.28        13.94        32.75        29.19 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3494 
       22.09        32.71        25.08        21.76        20.12         1.02 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        58.03        62.96         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       24.03        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 
       12.99        24.00        23.01        13.94        19.99         6.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3819 
       47.01        11.01        36.00         5.03        35.05        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3976 TCGA-AA-3986 
       17.98        38.99        24.03        18.05        26.01        19.07 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01V 
        7.96        19.00        17.03        17.03         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A02J TCGA-AA-A02K TCGA-AD-6548 TCGA-AD-6964 TCGA-AD-6965 
       26.01         5.03        14.01        21.37         0.76         0.20 
TCGA-AM-5821 TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-CA-5256 TCGA-CA-5797 
        0.92        16.31         1.41         6.77         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
        0.07         0.26       102.44        21.99         8.02        13.02 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-D5-5538 
       22.98         5.03        15.02        29.03        21.99        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
       13.51        11.51         1.32        17.13        14.30        13.41 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F 
       38.20       130.65       131.51       139.17         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6807 TCGA-G4-6295 
       60.79       117.07        13.38        13.64        16.24         8.35 
TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6323 TCGA-AF-2687 
       23.51        55.04        35.93        36.72        13.78        24.13 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       17.95        13.55         8.45        36.03        32.02         8.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3727 TCGA-AG-3731 
        1.02         2.01        46.03        34.03         0.99         1.02 
TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-A00C TCGA-AG-A01Y 
        0.99        35.01        14.01        36.03         6.02        64.01 
TCGA-AG-A025 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       49.97       117.11         0.20         0.69         6.05         6.05 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        13.97        60.03        15.02        12.99        13.97 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6513 
       57.24       129.27         0.49        20.55        20.91        16.34 
TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6641 
       14.86         0.39        26.43 

$subtype3
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        46.65        23.38        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3808 
       15.52        37.05        37.25        16.04        34.65        33.34 
TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3510 
       36.53        32.45         5.03         3.02        37.05        63.98 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3543 
       13.02        37.05        36.03         8.05        19.07         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-3558 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       20.98        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.05        15.02         5.98        37.05        19.00 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       26.99         0.99         0.99        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       15.95        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-3862 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        29.98        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-3970 TCGA-AA-3971 
       20.98        34.03         2.01        21.99        36.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       27.02        27.02        18.05        27.02        42.02        14.99 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01T 
        0.99        32.02        12.00        38.07        35.01        33.04 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.06        51.98        39.98         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 
       39.98        18.05        40.96         0.95        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         5.65        32.94        83.80        22.36        65.00 
TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 
       70.16        20.02        37.02         8.02        26.04        29.06 
TCGA-D5-6932 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3581 
       11.38        43.04        12.72        10.39        12.00         7.07 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       24.00         1.02        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3883 
       15.95        19.99        19.99        29.98        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       36.95        17.03         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02        36.03         9.07        12.00        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-EI-6507 
       10.98         1.94        38.96        61.97        41.00        19.96 

subtype1 subtype2 subtype3 
    0.07     0.07     0.92 
subtype1 subtype2 subtype3 
  140.38   139.17    83.80 
subtype1 subtype2 subtype3 
   16.14    17.95    24.00 
[1] "0.1 - 140.4 (16.1)" "0.1 - 139.2 (17.9)" "0.9 - 83.8 (24.0)" 
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1 176  51
  subtype2 100  43
  subtype3 129  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  176   51
  subtype2  100   43
  subtype3  129   46
        clus
vv       subtype1 subtype2 subtype3
  COLON       176      100      129
  RECTUM       51       43       46
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      36        0       10        78         4         1         8
  subtype2      22        1        6        34         2         1         7
  subtype3      36        0       20        42         4         0        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          8         28         18       13        14         1
  subtype2          6         21         14       23         4         0
  subtype3          2         20         13       21         5         0
D10V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          36       22       36
  STAGE IA          0        1        0
  STAGE II         10        6       20
  STAGE IIA        78       34       42
  STAGE IIB         4        2        4
  STAGE IIC         1        1        0
  STAGE III         8        7       12
  STAGE IIIA        8        6        2
  STAGE IIIB       28       21       20
  STAGE IIIC       18       14       13
  STAGE IV         13       23       21
  STAGE IVA        14        4        5
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   8  37 158  25
  subtype2   6  22 101  14
  subtype3   6  36 117  17
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        6        6
  T2       37       22       36
  T3      158      101      117
  T4       25       14       17
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 138  53  35
  subtype2  69  42  32
  subtype3 106  38  32
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      138       69      106
  N1       53       42       38
  N2       35       32       32
[1] 3 3
[1] 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
  subtype1 163  19   5   1  36
  subtype2 103  25   2   0  13
  subtype3 146  24   2   0   1
D10V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       163      103      146
  M1        19       25       24
  M1A        5        2        2
  M1B        1        0        0
  MX        36       13        1
[1] 5 3
[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
  subtype1 101 128
  subtype2  72  72
  subtype3  84  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101  128
  subtype2   72   72
  subtype3   84   92
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      101       72       84
  MALE        128       72       92
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                  151                            25
  subtype2                   90                             9
  subtype3                  110                            19
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    49                              2
  subtype2                    40                              3
  subtype3                    38                              5
D10V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                151       90      110
  COLON MUCINOUS ADENOCARCINOMA        25        9       19
  RECTAL ADENOCARCINOMA                49       40       38
  RECTAL MUCINOUS ADENOCARCINOMA        2        3        5
[1] 4 3
[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
  subtype1   6 223
  subtype2   1 143
  subtype3   2 174
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  223
  subtype2    1  143
  subtype3    2  174
     clus
vv    subtype1 subtype2 subtype3
  NO         6        1        2
  YES      223      143      174
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 142   2   4  17
  subtype2  95   1  15   7
  subtype3 147   2  17   2
D10V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142       95      147
  R1        2        1        2
  R2        4       15       17
  RX       17        7        2
[1] 4 3
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        15
  subtype2                                0     4                         7
  subtype3                                0     0                         4
          vv
clus       WHITE
  subtype1   181
  subtype2    68
  subtype3    31
D10V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   8        4        0
  BLACK OR AFRICAN AMERICAN              15        7        4
  WHITE                                 181       68       31
[1] 4 3
[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 = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 17  6
  subtype2 14  6
  subtype3 22  6
  subtype4 17 10
  subtype5 14  4
  subtype6 13  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      23       20       28       27       18       17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        6        6       10        4        4 
$subtype1
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-AD-6965 TCGA-D5-5537 
       43.43        27.09        24.13        20.61         0.20        14.99 
TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 
      130.65         7.50        35.97        33.67        28.21         8.35 
TCGA-G4-6306 TCGA-AF-6672 TCGA-AG-3732 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       44.68        10.39        32.98         7.99        11.01        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A1DG TCGA-EI-6511 TCGA-EI-6513 
       36.00         7.10        51.48        15.85        16.34 

$subtype2
TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3489 TCGA-AD-5900 
       31.63        22.52        21.76        23.87         1.02         0.07 
TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6167 
        0.20         1.41         5.13         3.19        27.02        14.99 
TCGA-CM-6674 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 
       12.95         1.55        16.31        16.24         1.28        43.07 
TCGA-G4-6314 TCGA-G4-6627 
       35.93        47.15 

$subtype3
TCGA-A6-5667 TCGA-CA-6719 TCGA-D5-6922 TCGA-F4-6459 TCGA-F4-6460 TCGA-G4-6303 
       29.16         1.35        10.13         8.61        13.38        61.87 
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-3731 TCGA-AG-4022 TCGA-AH-6549 
       24.13        37.74        14.50         1.02         0.99         0.20 
TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE 
        6.05         6.05        12.95        10.06        57.24       129.27 
TCGA-EI-6509 TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.00        16.31         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6572 
        0.39         1.02         0.66        47.08 

$subtype4
TCGA-A6-6141 TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-6605 TCGA-CM-6677 TCGA-CM-6678 
        8.38         0.10         0.76         5.23        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.06        12.03        24.43        38.20        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A280 TCGA-G4-6299 TCGA-G4-6625 TCGA-AF-6655 TCGA-AH-6544 
      140.38         7.76        74.56        91.79        20.02         0.49 
TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 
        1.45        10.19         4.73        13.05        41.36        32.61 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$subtype5
TCGA-A6-6142 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-AZ-5403 
       25.08        19.66        20.28         6.97         1.02        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-6748 TCGA-CM-5860 TCGA-CM-6676 TCGA-D5-6534 
       12.10        29.56         2.01        16.01        11.08         7.92 
TCGA-D5-6924 TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6569 TCGA-DC-5869 TCGA-DC-6156 
       14.30       139.17         6.12        13.45        12.99        15.02 

$subtype6
TCGA-A6-6649 TCGA-A6-6653 TCGA-AD-6548 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6601 
       24.16        24.39        21.37        56.55        49.41       100.01 
TCGA-CA-6718 TCGA-CK-5916 TCGA-D5-6533 TCGA-D5-6536 TCGA-DM-A1HA TCGA-F4-6570 
        0.10        21.14         1.32        17.85       131.51         6.18 
TCGA-G4-6309 TCGA-G4-6628 TCGA-AH-6643 TCGA-EI-6506 TCGA-EI-6507 
       51.75        52.80         0.69        20.55        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.20     0.07     0.20     0.10     1.02     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  130.65    47.15   129.27   140.38   139.17   131.51 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  20.610   15.615   13.165   12.590   13.875   21.370 
[1] "0.2 - 130.7 (20.6)" "0.1 - 47.1 (15.6)"  "0.2 - 129.3 (13.2)"
[4] "0.1 - 140.4 (12.6)" "1.0 - 139.2 (13.9)" "0.1 - 131.5 (21.4)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 13 11
  subtype2 20  0
  subtype3  6 22
  subtype4 16 12
  subtype5 16  2
  subtype6 14  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   11
  subtype2   20    0
  subtype3    6   22
  subtype4   16   12
  subtype5   16    2
  subtype6   14    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  COLON        13       20        6       16       16       14
  RECTUM       11        0       22       12        2        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       6        1         7         0         0         1          0
  subtype2       2        1         4         0         0         0          0
  subtype3       0        1         8         0         0         0          1
  subtype4       1        0        10         0         1         1          3
  subtype5       2        2         4         1         0         0          0
  subtype6       4        2         6         0         0         0          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          1        2         1
  subtype2          4          4        4         1
  subtype3          5          4        4         4
  subtype4          4          2        0         1
  subtype5          1          1        3         2
  subtype6          3          2        0         0
D11V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           6        2        0        1        2        4
  STAGE II          1        1        1        0        2        2
  STAGE IIA         7        4        8       10        4        6
  STAGE IIB         0        0        0        0        1        0
  STAGE IIC         0        0        0        1        0        0
  STAGE III         1        0        0        1        0        0
  STAGE IIIA        0        0        1        3        0        0
  STAGE IIIB        4        4        5        4        1        3
  STAGE IIIC        1        4        4        2        1        2
  STAGE IV          2        4        4        0        3        0
  STAGE IVA         1        1        4        1        2        0
[1] 11  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  5 15  2
  subtype2  0  2 16  2
  subtype3  0  0 26  2
  subtype4  1  3 21  3
  subtype5  0  3 10  5
  subtype6  1  3 12  1
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        2        0        0        1        0        1
  T2        5        2        0        3        3        3
  T3       15       16       26       21       10       12
  T4        2        2        2        3        5        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 14  6  4
  subtype2  7  5  8
  subtype3  9 10  8
  subtype4 13 10  5
  subtype5 10  6  2
  subtype6 13  2  2
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       14        7        9       13       10       13
  N1        6        5       10       10        6        2
  N2        4        8        8        5        2        2
[1] 3 6
[1] 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 MX
  subtype1 17  2   0  5
  subtype2 11  5   0  3
  subtype3 17  6   1  4
  subtype4 18  1   1  5
  subtype5  8  3   2  5
  subtype6 16  0   0  1
D11V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0        17       11       17       18        8       16
  M1         2        5        6        1        3        0
  M1A        0        0        1        1        2        0
  MX         5        3        4        5        5        1
[1] 4 6
[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
  subtype1  8 16
  subtype2  9 11
  subtype3 15 14
  subtype4 12 16
  subtype5  7 11
  subtype6  7 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   16
  subtype2    9   11
  subtype3   15   14
  subtype4   12   16
  subtype5    7   11
  subtype6    7   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        8        9       15       12        7        7
  MALE         16       11       14       16       11       10
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   13                             0
  subtype2                   16                             4
  subtype3                    6                             0
  subtype4                   14                             2
  subtype5                   12                             4
  subtype6                   14                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    11                              0
  subtype2                     0                              0
  subtype3                    22                              0
  subtype4                    11                              1
  subtype5                     2                              0
  subtype6                     3                              0
D11V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 13       16        6       14       12
  COLON MUCINOUS ADENOCARCINOMA         0        4        0        2        4
  RECTAL ADENOCARCINOMA                11        0       22       11        2
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        0        1        0
                                clus
vv                               subtype6
  COLON ADENOCARCINOMA                 14
  COLON MUCINOUS ADENOCARCINOMA         0
  RECTAL ADENOCARCINOMA                 3
  RECTAL MUCINOUS ADENOCARCINOMA        0
[1] 4 6
[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
  subtype1  1 23
  subtype2  0 20
  subtype3  2 27
  subtype4  1 27
  subtype5  0 18
  subtype6  0 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    0   20
  subtype3    2   27
  subtype4    1   27
  subtype5    0   18
  subtype6    0   17
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         1        0        2        1        0        0
  YES       23       20       27       27       18       17
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 12  0  0  2
  subtype2 14  0  0  0
  subtype3 18  0  2  2
  subtype4 11  1  0  0
  subtype5  9  0  0  1
  subtype6  9  0  0  2
D11V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       12       14       18       11        9        9
  R1        0        0        0        1        0        0
  R2        0        0        2        0        0        0
  RX        2        0        2        0        1        2
[1] 4 6
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                1     0                         2
  subtype3                                0     1                         0
  subtype4                                0     0                         1
  subtype5                                0     0                         2
  subtype6                                0     2                         1
          vv
clus       WHITE
  subtype1    20
  subtype2    16
  subtype3    25
  subtype4    27
  subtype5    15
  subtype6    14
D11V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        0        1        0        0
  BLACK OR AFRICAN AMERICAN               2        2        0        1        2
  WHITE                                  20       16       25       27       15
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   2
  BLACK OR AFRICAN AMERICAN               1
  WHITE                                  14
[1] 4 6
[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 = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 38 17
  subtype2 12  3
  subtype3 24  9
  subtype4 23  7
subtype1 subtype2 subtype3 subtype4 
      55       15       33       30 
subtype1 subtype2 subtype3 subtype4 
      17        3        9        7 
$subtype1
TCGA-A6-2675 TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       43.43        31.63        22.52         8.38        24.16        21.76 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-5900 TCGA-AD-6548 
       23.87        19.66        20.28         1.02         0.07        21.37 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 
        1.02         0.10         0.76         0.20         1.41         5.13 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-6167 
        0.10        21.14         2.01        27.02        16.01        14.99 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6534 
       12.95        11.08        11.01        10.06        12.03         7.92 
TCGA-D5-6536 TCGA-DM-A280 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       17.85         7.76        13.45         6.18         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6314 TCGA-G4-6625 
       16.24         1.28        74.56        43.07        35.93        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-AG-3732 TCGA-AH-6547 TCGA-DC-6157 TCGA-DC-6158 
       47.15        52.80        32.98         1.45        36.00         7.10 
TCGA-F5-6464 
        9.96 

$subtype2
TCGA-A6-5667 TCGA-CA-6719 TCGA-D5-6922 TCGA-F4-6459 TCGA-G4-6303 TCGA-AF-3911 
       29.16         1.35        10.13         8.61        61.87        37.74 
TCGA-AF-4110 TCGA-AG-4022 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE 
       14.50         0.99        12.95        10.06        57.24       129.27 
TCGA-EI-6514 TCGA-F5-6571 TCGA-F5-6812 
       16.31        31.30         0.66 

$subtype3
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6965 
       27.09        24.13        20.61        24.39        56.55         0.20 
TCGA-AZ-6598 TCGA-D5-5537 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.41        14.99        24.43       130.65         7.50       131.51 
TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 
       35.97        33.67        28.21         8.35        44.68        51.75 
TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-5918 
       10.39         0.49         0.69        10.19         4.73         7.99 
TCGA-DC-4749 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       11.01        51.48        32.61        19.96        15.85        16.34 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$subtype4
TCGA-A6-6142 TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF 
       25.08         6.97        11.08         1.32        14.30        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6460 
       13.32        12.59       140.38       139.17         6.12        13.38 
TCGA-AF-2687 TCGA-AF-6655 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       24.13        20.02         1.02         0.20         6.05         6.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EI-6506 
       15.02        12.99        15.02        13.05        41.36        20.55 
TCGA-EI-6509 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6572 
       17.00        37.51        14.86         0.39         1.02        47.08 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.66     0.20     0.20 
subtype1 subtype2 subtype3 subtype4 
  100.01   129.27   131.51   140.38 
subtype1 subtype2 subtype3 subtype4 
   13.45    14.50    24.13    13.84 
[1] "0.1 - 100.0 (13.4)" "0.7 - 129.3 (14.5)" "0.2 - 131.5 (24.1)"
[4] "0.2 - 140.4 (13.8)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 50  5
  subtype2  5  9
  subtype3 18 16
  subtype4 12 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    5
  subtype2    5    9
  subtype3   18   16
  subtype4   12   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON        50        5       18       12
  RECTUM        5        9       16       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       9        3        15         1         0         0          0
  subtype2       0        1         5         0         0         0          1
  subtype3       4        2         9         0         1         1          2
  subtype4       2        1        10         0         0         1          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          7          7        6         2
  subtype2          4          1        1         2
  subtype3          7          3        2         1
  subtype4          3          3        4         4
D12V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           9        0        4        2
  STAGE II          3        1        2        1
  STAGE IIA        15        5        9       10
  STAGE IIB         1        0        0        0
  STAGE IIC         0        0        1        0
  STAGE III         0        0        1        1
  STAGE IIIA        0        1        2        1
  STAGE IIIB        7        4        7        3
  STAGE IIIC        7        1        3        3
  STAGE IV          6        1        2        4
  STAGE IVA         2        2        1        4
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  9 36  9
  subtype2  0  0 14  1
  subtype3  2  5 25  2
  subtype4  1  2 25  3
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        0        2        1
  T2        9        0        5        2
  T3       36       14       25       25
  T4        9        1        2        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 31 12 12
  subtype2  6  5  4
  subtype3 15 12  7
  subtype4 14 10  6
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31        6       15       14
  N1       12        5       12       10
  N2       12        4        7        6
[1] 3 4
[1] 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 MX
  subtype1 34  7   1 11
  subtype2 10  1   1  3
  subtype3 23  3   0  7
  subtype4 20  6   2  2
D12V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        34       10       23       20
  M1         7        1        3        6
  M1A        1        1        0        2
  MX        11        3        7        2
[1] 4 4
[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
  subtype1 23 32
  subtype2  9  6
  subtype3 11 23
  subtype4 15 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   32
  subtype2    9    6
  subtype3   11   23
  subtype4   15   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23        9       11       15
  MALE         32        6       23       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   42                             8
  subtype2                    5                             0
  subtype3                   18                             0
  subtype4                   10                             2
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     5                              0
  subtype2                     9                              0
  subtype3                    15                              1
  subtype4                    20                              0
D12V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 42        5       18       10
  COLON MUCINOUS ADENOCARCINOMA         8        0        0        2
  RECTAL ADENOCARCINOMA                 5        9       15       20
  RECTAL MUCINOUS ADENOCARCINOMA        0        0        1        0
[1] 4 4
[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
  subtype1  0 55
  subtype2  1 14
  subtype3  2 32
  subtype4  1 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   55
  subtype2    1   14
  subtype3    2   32
  subtype4    1   31
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        2        1
  YES       55       14       32       31
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 33  0  0  3
  subtype2 11  0  0  1
  subtype3 13  1  0  2
  subtype4 16  0  2  1
D12V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       33       11       13       16
  R1        0        0        1        0
  R2        0        0        0        2
  RX        3        1        2        1
[1] 4 4
[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 BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         5
  subtype2                                0     1                         0
  subtype3                                0     1                         2
  subtype4                                0     0                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    13
  subtype3    30
  subtype4    28
D12V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        1        1        0
  BLACK OR AFRICAN AMERICAN               5        0        2        1
  WHITE                                  46       13       30       28
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
