[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/10005910/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/10668129/COADREAD-TP.mergedcluster.txt"

nPatients in clinical file=612, in cluster file=616, common to both=608
[1]  12 608
[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   4 
234 214 109  35 
  1   2   3   4 
234 214 109  35 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 98 156 119 
  1   2   3 
 98 156 119 
[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 
128 131 141 193 
  1   2   3   4 
128 131 141 193 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 64 107  45  67  65 101 144 
  1   2   3   4   5   6   7 
 64 107  45  67  65 101 144 
[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 
101 109  85 
  1   2   3 
101 109  85 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
82 53 67 33 60 
 1  2  3  4  5 
82 53 67 33 60 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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 608 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
         154         1126         1419         1331         1321          711 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
         541         1286         1366         1068         1387           NA 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3808 
         472         1127         1133          488         1054         1014 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
         996         1111           NA          987         1001          962 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
         926          888         1020          718          672          671 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
         995          887          824          685          734          255 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
         763          766          735          627          662          751 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
         742          726          612          598          617           NA 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
          NA           NA         1595          293           NA           31 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
          NA           31         1127           31         1065         1765 
TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1915         1946          212           31           NA         1186 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 
          31          276          731           NA         1127         1096 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
         245          580           NA           NA          580         1035 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
         882          882          791          395           30          426 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        1034          639           NA          730          546          911 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
         700          638          608          424          608         1856 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
        2375          184          212         1643           NA          426 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
          28         1522         1431         1430          457           NA 
TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 
         182           NA         1127          578           NA           NA 
TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 
          NA           NA         2587          821           NA          579 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3815 TCGA-AA-3818 
          30           30         1066           NA         1005           NA 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
         761           31          547          485         1186         1124 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
        1126          454           NA          518           30           NA 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        1006           NA         1096          975           30          945 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
         945           NA          914         1612          518          731 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA          912           NA          549          943           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
         395          730         1004          791          730           NA 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 
         638         1035           61          669         1096          489 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        1551          397         1036          791          761          730 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
         822          822           NA          580           NA          822 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
         424         1157          578          913         1035          549 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
         549          518           NA          822         1278           30 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
         518          456          669         1064          457          457 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
          30          974          365          943          943           NA 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
          31         1065           31         1005         1065          791 
TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1126           NA           NA         1581           NA         1216 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
          NA           NA           NA           28           NA         1247 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        1216           NA         1246            2          650          128 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        1720           24           22           48           31            3 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
          23            6           NA           13           14           28 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
         441          824           NA           NA          479            6 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
         652          542          158          168         2289         1532 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
        1776           NA           NA         1002           NA         2549 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
          NA         1977           NA         1868           NA           NA 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
          NA           68           93           65           99          100 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
           2            8           10            3           41          534 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        3116         1227         2134          475         1466         1561 
TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 
         669           NA           NA           NA           89           61 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
        3780          701          609         1126          244          792 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
         244          822          396          884          670          699 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
         915          487          457           NA          457          457 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
         518          457          365          427          883          488 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
         669          456          395          396          457          427 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
         335          394          397          337          337          335 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
         306          366          456          373          596          411 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
         350          614          621          540          555           40 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
         241          460          543          137          521          380 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
         491          474          229          377          308          378 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
         435          275          287          354          408           46 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
         365          346          312         3641          743         1162 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
        3974         2821         1518          405          383         4270 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
         228         1348         4000         4126          236         4233 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
         186          427          805         2475         3648         1094 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
        1849         3561         2988         2895           NA          407 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
          NA          415          409           NA         1091           47 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
         496          900          494         1024           39           16 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        1077          591         3275           NA          254         2506 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
          NA         2268         1310         1882         1631         1359 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
        1674         1574         1372         1199         1093         1117 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
        1095          804          672          792          419         1089 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
         796         2792           NA         1434         1606          125 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
         154           85          182          170          821          526 
TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
         449          734          546          524         1309          412 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-4110 
         581          387         1148           NA         1146          441 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
         257          468          609          316         2635         2007 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
         360           NA          365          974          244          215 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
          31           61           NA           31         1400           NA 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
          NA         1035           NA         1522          366          184 
TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
          NA           NA           30          485          608           NA 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
         608           NA          243           30          912           31 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
        1003           30           30           NA          608           31 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3891 TCGA-AG-3892 TCGA-AG-3893 
          NA         1124          518          548          396         1065 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
         426           31         1461           NA          974          608 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 
         853         1096          427           31          518           NA 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
          NA           30          638          424          183          790 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
         700         1126          485         1096          276           31 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
         365          943         2130         1947          334           NA 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1520           NA           NA         1885         1247         1157 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
        3562           15           44            6           21           22 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
         140           55          310          184          184           NA 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
         212          285          144          425         1826          243 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
         334          335          457          395          365          425 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
         457         1095          216          914          394          397 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
         306          161         3846         1258         1741         3932 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
         734         1566          992           15           73          625 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
         607          636          517          556          482          538 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
         497          496          499          262          350          328 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
         415          531          364          257           NA         1141 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
         952          452           12           31           20           21 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
          16           34           23           14           NA         1696 
TCGA-G5-6572 TCGA-G5-6641 
          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=96,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=344,	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=8,	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=1,	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=30,	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 608 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=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  19 107 415  64 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   20   107   415    64 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  19 107 415  64 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   20   107   415    64 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
346 146 112 
[1] "table(vv)"
vv
 N0  N1  N2 
346 146 112 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
346 146 112 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
346 146 112 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 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       T0+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
  T0+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       T0+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
  T0+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 179  45
  subtype2 169  33
  subtype3  82  22
  subtype4  27   6
subtype1 subtype2 subtype3 subtype4 
     224      202      104       33 
subtype1 subtype2 subtype3 subtype4 
      45       33       22        6 
$subtype1
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 
        5.06        46.65        43.76        23.38        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       37.25        16.04        31.63        33.53        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        24.16        21.76        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         1.02         3.02        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       13.02         1.02        24.03        37.05         8.05        19.07 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
       29.00         0.99        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 
        6.97         0.92        47.05        11.01        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
       15.95        38.99        14.93        36.03        32.05        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-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-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       34.98         0.99        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       35.01        39.06        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
       21.37        56.55         0.79         0.72         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
        0.92        27.09         0.20        17.82        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        1.41        32.94         5.13         6.77        12.10       100.01 
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        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       22.03        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       12.99        14.04        12.95        13.05        11.01        12.03 
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-A288 
       13.32       140.38       135.65         7.76       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       81.37        60.79        95.18        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6856 
        6.18        35.87         1.55        29.59        16.24        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-AF-2691 TCGA-AF-3400 
       52.80         2.79         5.98        14.76        43.04        12.72 
TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3600 
        8.45        12.00         8.02         2.01        12.03         6.05 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A020 
        0.99        13.02        14.01        20.98        13.94        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         0.49         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 
       10.19         6.05         4.73        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        5.29        32.61        20.55        19.96        20.91        18.28 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6814 
        8.61        10.78        17.46         8.45         9.96         0.53 
TCGA-F5-6861 TCGA-G5-6235 
        1.12        55.76 

$subtype2
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       15.52        34.65        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       29.19        23.61        32.71        29.16        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.08        20.61        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 
       52.44         5.03         6.97        38.99         9.07        34.03 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3560 
       29.00        12.99        14.01        21.01        24.00        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 
       13.94        19.99         2.01        14.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       19.00        85.05        25.02        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3955 TCGA-AA-3956 
        0.99        31.07        24.03        27.02        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       34.03        17.03        42.02        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E 
       15.02        32.02        12.00        31.00        33.04         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6901 TCGA-AD-6963 
       39.98         2.01        40.96         4.21         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
        0.20         0.43        14.50         0.95        15.75         5.19 
TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6715 
       75.25        22.36        29.56         5.23         1.94         0.07 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5860 
       48.20        21.99         2.01         8.02        13.02        16.01 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5538 
       17.03        14.04        29.03        15.02        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6932 
       19.59        13.51        18.25         1.32        15.12        11.38 
TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 
      130.65       131.51        26.47       119.93        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 
       13.38        33.67         1.28         0.53        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       82.39        61.87        44.68        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       36.72        36.00        46.75         4.11         5.06         5.59 
TCGA-QG-A5YV TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       26.99        17.95        13.55        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       14.50        15.39         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-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
        0.99         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G 
        9.07        12.00        31.00        70.03         1.94        38.96 
TCGA-AG-A032 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 
       38.04         6.97         9.37        13.97         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6683 TCGA-DY-A0XA 
       11.01        12.99        12.00        15.02        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6512 
       41.36       129.27        24.13        51.48         2.40        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 
       16.34        16.31        16.41        11.97        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
        1.02         0.66         0.69         0.76 

$subtype3
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 
       43.43        27.09        25.18         9.63         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3538 
        1.02        35.01         1.02        36.03        19.07        26.01 
TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3678 
       33.99        20.98        78.08         6.05        54.02        47.01 
TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3858 TCGA-AA-3870 TCGA-AA-3939 
        5.98        36.00         5.03        31.07        29.98        12.99 
TCGA-AA-3941 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00U 
       24.00        24.00        27.02        19.00        18.05        17.03 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        1.02        37.02        51.98         5.03         0.92        41.00 
TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        1.58        21.44         5.65        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6719 TCGA-CK-4952 
       61.41        49.41        11.74         2.24         1.35        15.62 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6172 
       22.98        30.08         5.03        21.99        13.02        11.01 
TCGA-CM-6676 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 
       11.08        11.51         4.50        17.13        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA 
       10.13        12.43         9.04       119.70        38.20         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6805 TCGA-G4-6299 
       44.32         6.12       117.07        98.24        16.31        74.56 
TCGA-G4-6307 TCGA-QG-A5YX TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       55.04        17.29        20.02        10.39        36.03        32.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3732 
       24.00         1.02         2.01         0.99         7.99        32.98 
TCGA-AG-3887 TCGA-AG-3902 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A023 TCGA-AH-6643 
       36.95        32.02         1.02        64.01        51.98         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CL-5917 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DD 
        0.72         6.05        60.03         7.10        13.05        57.24 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6864 
        0.49        17.00        15.85        11.51        14.86         0.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$subtype4
TCGA-A6-4107 TCGA-AA-3552 TCGA-AA-3673 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 
       32.45        13.02        50.04        33.07         0.99        17.03 
TCGA-AA-A004 TCGA-AA-A01X TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-6607 TCGA-CA-5256 
       13.94        26.01        16.31         5.52         3.19         2.14 
TCGA-CA-5797 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5864 TCGA-CM-6165 TCGA-CM-6677 
        3.29         8.02        29.06        15.02        16.04        11.08 
TCGA-D5-5537 TCGA-DM-A1D8 TCGA-F4-6855 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2690 
       14.99        12.59        35.41        91.79        24.13        17.23 
TCGA-AG-3731 TCGA-AG-3898 TCGA-AG-A011 TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6157 
        1.02        48.03        37.02        41.00        13.97        36.00 
TCGA-EI-6885 TCGA-F5-6465 TCGA-G5-6572 
       13.64        37.51        47.08 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.46     0.99 
subtype1 subtype2 subtype3 subtype4 
  140.38   131.51   119.70    91.79 
subtype1 subtype2 subtype3 subtype4 
  17.835   19.050   18.165   16.310 
[1] "0.1 - 140.4 (17.8)" "0.1 - 131.5 (19.1)" "0.5 - 119.7 (18.2)"
[4] "1.0 - 91.8 (16.3)" 
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1 193  41
  subtype2 136  74
  subtype3  76  33
  subtype4  24  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  193   41
  subtype2  136   74
  subtype3   76   33
  subtype4   24   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       193      136       76       24
  RECTUM       41       74       33       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 IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      50        1       16        75         6         0        10
  subtype2      30        0        8        53         3         1        10
  subtype3      17        0       11        24         1         2         5
  subtype4       5        0        1        13         0         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         26         17       12         7         1
  subtype2          8         37         20       29        11         0
  subtype3          4         12         11       15         6         0
  subtype4          3          1          4        4         1         0
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          50       30       17        5
  STAGE IA          1        0        0        0
  STAGE II         16        8       11        1
  STAGE IIA        75       53       24       13
  STAGE IIB         6        3        1        0
  STAGE IIC         0        1        2        0
  STAGE III        10       10        5        1
  STAGE IIIA        7        8        4        3
  STAGE IIIB       26       37       12        1
  STAGE IIIC       17       20       11        4
  STAGE IV         12       29       15        4
  STAGE IVA         7       11        6        1
  STAGE IVB         1        0        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       T0+T1  T2  T3  T4
  subtype1    10  46 150  27
  subtype2     8  33 151  22
  subtype3     2  18  78  11
  subtype4     0   8  24   2
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       10        8        2        0
  T2          46       33       18        8
  T3         150      151       78       24
  T4          27       22       11        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"
          vv
clus        N0  N1  N2
  subtype1 155  45  34
  subtype2 103  68  42
  subtype3  57  25  26
  subtype4  20   8   6
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      155      103       57       20
  N1       45       68       25        8
  N2       34       42       26        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 M1B  MX
  subtype1 187  15   2   1  25
  subtype2 152  36   3   0  21
  subtype3  78  17   3   0  10
  subtype4  26   4   1   0   2
D3V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0       187      152       78       26
  M1        15       36       17        4
  M1A        2        3        3        1
  M1B        1        0        0        0
  MX        25       21       10        2
[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"
D3V8, binary
          cls
clus         0   1
  subtype1 113 121
  subtype2  97 117
  subtype3  50  59
  subtype4  17  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113  121
  subtype2   97  117
  subtype3   50   59
  subtype4   17   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      113       97       50       17
  MALE        121      117       59       18
[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                  146                            46
  subtype2                  133                             3
  subtype3                   70                             6
  subtype4                   24                             0
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    31                              9
  subtype2                    74                              0
  subtype3                    27                              4
  subtype4                    11                              0
D3V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                146      133       70       24
  COLON MUCINOUS ADENOCARCINOMA        46        3        6        0
  RECTAL ADENOCARCINOMA                31       74       27       11
  RECTAL MUCINOUS ADENOCARCINOMA        9        0        4        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"
D3V10, binary
          cls
clus         0   1
  subtype1   2 232
  subtype2   3 211
  subtype3   3 106
  subtype4   1  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  232
  subtype2    3  211
  subtype3    3  106
  subtype4    1   34
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        3        3        1
  YES      232      211      106       34
[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 176   3   6  13
  subtype2 152   1  17   6
  subtype3  72   0  11   5
  subtype4  26   1   2   3
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      176      152       72       26
  R1        3        1        0        1
  R2        6       17       11        2
  RX       13        6        5        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"
D3V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                        22
  subtype2                                0     1                        16
  subtype3                                0     2                         3
  subtype4                                0     2                         3
          vv
clus       WHITE
  subtype1   120
  subtype2   100
  subtype3    54
  subtype4    18
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   7        1        2        2
  BLACK OR AFRICAN AMERICAN              22       16        3        3
  WHITE                                 120      100       54       18
[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(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  81  16
  subtype2 122  31
  subtype3  92  22
subtype1 subtype2 subtype3 
      97      153      114 
subtype1 subtype2 subtype3 
      16       31       22 
$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-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3742 
       37.74        15.39        86.63        65.98        11.84         0.99 
TCGA-AG-4022 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A036 TCGA-AH-6549 TCGA-AH-6643 
        0.99        10.98         1.94       117.11         0.20         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        0.72         4.60         1.81         6.97        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A0XA 
       13.97        15.02        36.00         7.10        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24       129.27        51.48        32.61         2.40 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6885 
       15.85        16.34        16.31        16.41        11.51        13.64 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
       11.97        37.51        31.30         0.39         1.02         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6641 
        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        21.01         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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-AG-3731 
        5.06         2.79         5.98         5.59        14.76         1.02 
TCGA-AG-A01W TCGA-AG-A02N TCGA-CI-6620 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 
       70.03        61.97         6.05         5.29        24.13         0.49 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-F5-6814 TCGA-G5-6233 
       20.91        18.28        17.69         8.61         0.53        18.28 

subtype1 subtype2 subtype3 
    0.10     0.07     0.07 
subtype1 subtype2 subtype3 
  102.44   139.17   140.38 
subtype1 subtype2 subtype3 
  14.990   17.030   17.345 
[1] "0.1 - 102.4 (15.0)" "0.1 - 139.2 (17.0)" "0.1 - 140.4 (17.3)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  68  28
  subtype2 104  52
  subtype3 103  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   28
  subtype2  104   52
  subtype3  103   16
        clus
vv       subtype1 subtype2 subtype3
  COLON        68      104      103
  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        41         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         10         26         13       12        12         0
  subtype3          2         15         10        8         5         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       41       38
  STAGE IIB         1        2        4
  STAGE IIC         0        2        1
  STAGE III         1        5        5
  STAGE IIIA        7       10        2
  STAGE IIIB       13       26       15
  STAGE IIIC       11       13       10
  STAGE IV          6       12        8
  STAGE IVA         7       12        5
  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       T0+T1  T2  T3  T4
  subtype1     3  11  68  15
  subtype2     5  22 112  17
  subtype3     3  22  80  13
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        3        5        3
  T2          11       22       22
  T3          68      112       80
  T4          15       17       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"
          vv
clus       N0 N1 N2
  subtype1 52 28 17
  subtype2 80 47 26
  subtype3 73 24 22
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       52       80       73
  N1       28       47       24
  N2       17       26       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  26
  subtype3  85  10   1   1  19
D4V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        70      105       85
  M1         9       19       10
  M1A        2        5        1
  M1B        0        0        1
  MX        14       26       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 88
  subtype3 64 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   60
  subtype2   68   88
  subtype3   64   55
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       68       64
  MALE         60       88       55
[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                   98                             6
  subtype3                   88                            15
          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       98       88
  COLON MUCINOUS ADENOCARCINOMA        12        6       15
  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   4 152
  subtype3   0 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   94
  subtype2    4  152
  subtype3    0  119
     clus
vv    subtype1 subtype2 subtype3
  NO         4        4        0
  YES       94      152      119
[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 101   1   2  11
  subtype3  74   2   4  13
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       67      101       74
  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                        17
  subtype3                                0     4                        17
          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       17       17
  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        21.01       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       T0+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
  T0+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        21.01       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       T0+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
  T0+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  96  28
  subtype2 103  20
  subtype3 105  31
  subtype4 154  27
subtype1 subtype2 subtype3 subtype4 
     124      123      136      181 
subtype1 subtype2 subtype3 subtype4 
      28       20       31       27 
$subtype1
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-A6-3810 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6142 
       33.34        36.53        31.63        22.09        22.52        25.08 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A56B 
       21.76        23.87        19.66        20.28        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3870 TCGA-AA-A01P TCGA-AD-5900 
        9.63         1.02         1.02        29.98        38.07         0.07 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 
       21.37         0.72         1.58         1.02         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
        0.92        27.09         0.20         1.41        32.94         5.13 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
      100.01         5.23         3.19         0.33         0.10         1.35 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-5349 
      102.44        70.16        21.01         2.01        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-AF-2687 TCGA-AF-2690 TCGA-AF-6655 TCGA-AG-3731 
       52.80         5.06        24.13        17.23        20.02         1.02 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 
        0.69         0.72        10.19        15.02         7.10         5.29 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6885 TCGA-EI-6917 
      129.27        24.13         2.40        19.96        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6864 
        0.66         0.69         0.53         0.46 

$subtype2
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-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3713 TCGA-AA-3833 
        6.97        54.02        11.01         5.98        19.04        15.95 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3939 
       33.07        36.03        32.05        30.05        53.00        12.99 
TCGA-AA-A00N TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 
        4.01        37.02        39.06        39.98        18.05        56.55 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
       15.75        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.65        65.00        61.41        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 
       11.74         2.24         3.06         3.25        17.56        40.34 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       15.62        51.32         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6171 TCGA-CM-6172 
       37.02        27.02        15.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6539 
       13.05        12.03        19.59        20.42        15.12        12.49 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 
       16.14        12.39        12.00       119.70        92.75        49.91 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M 
        7.50       135.65         7.76        14.04        98.24        95.18 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       29.59        19.43       107.67        53.62        44.68        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-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-3594 TCGA-AG-3599 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A008 
        2.01        12.03        32.98        13.02        32.02        13.94 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       61.97         0.49         1.45         1.81         6.05         6.05 
TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 
       30.05        20.55        18.28        17.69        16.41         8.61 
TCGA-EI-6884 TCGA-G5-6233 TCGA-G5-6641 
       10.78        18.28        26.43 

$subtype3
TCGA-A6-2677 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       17.79        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-A567 
       29.16        24.13        25.18        20.61        24.69        61.84 
TCGA-AA-3494 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3526 TCGA-AA-3534 
        1.02        62.96         6.97        38.99        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3867 
       26.01        78.08         6.05        37.05        85.05        24.03 
TCGA-AA-3955 TCGA-AA-A00O TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       20.98        27.02        26.01        39.98         5.03        14.01 
TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00         4.21         0.79         0.10         0.20         0.43 
TCGA-AU-3779 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 
       14.50        22.36        62.79        29.56         1.94         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4747 
        3.29         0.07         0.26        48.20        21.99         8.02 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       22.03         5.03        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
       29.03        21.99        15.02        11.08        11.01        14.99 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 
       13.51        18.25         1.32         4.50        17.13        14.30 
TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       13.41        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
       44.32       139.17         6.12        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6854 
       35.97        60.79       117.07        13.38        33.67         0.53 
TCGA-G4-6294 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       28.21        55.04        45.11        36.72        36.00        46.75 
TCGA-NH-A50T TCGA-QG-A5YV TCGA-AF-3911 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3742 
        4.11        26.99        37.74         8.45        36.03         0.99 
TCGA-AG-4022 TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6549 TCGA-AH-6897 
        0.99        31.00         1.94        38.96         0.20         4.60 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       36.00        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6509 
       57.24        51.48        32.61         0.49        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6810 
       15.85        16.34        16.31        11.51        11.97         0.39 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        55.76        47.08 

$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-A6-4107 TCGA-AA-3488 
       45.60        15.52        34.65        32.75        32.45         5.03 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 
        1.02         1.02         9.07        24.03        36.03        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 
       21.01        13.02        24.00        17.95        29.95        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       13.94        19.99         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
        0.99         0.99        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       17.03         0.99         0.99        31.07        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       36.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        17.03        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
        1.02        33.04        35.01        51.98         2.96         2.01 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 
        0.92        22.03        40.96        16.31         0.95        75.25 
TCGA-AZ-4681 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AF-2691 
       83.80        26.04         8.02        13.02        29.06        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       13.55        12.72        10.39        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02X TCGA-AG-A032 
       64.01        10.98        51.98        49.97        41.00        38.04 
TCGA-AG-A036 
      117.11 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.49     0.07     0.92 
subtype1 subtype2 subtype3 subtype4 
  131.51   135.65   140.38   117.11 
subtype1 subtype2 subtype3 subtype4 
   14.40    19.04    17.46    19.99 
[1] "0.1 - 131.5 (14.4)" "0.5 - 135.7 (19.0)" "0.1 - 140.4 (17.5)"
[4] "0.9 - 117.1 (20.0)"
D7V2, continuous
D7V3, binary
          cls
clus         0   1
  subtype1 100  28
  subtype2 103  26
  subtype3  95  46
  subtype4 131  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  100   28
  subtype2  103   26
  subtype3   95   46
  subtype4  131   60
        clus
vv       subtype1 subtype2 subtype3 subtype4
  COLON       100      103       95      131
  RECTUM       28       26       46       60
[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      12        0        5        44         2         0         2
  subtype2      28        1        9        41         2         1         8
  subtype3      23        0        8        30         2         2         4
  subtype4      38        0       13        53         5         0        13
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          5         17         17       14         6         0
  subtype2          6         15          4        6         7         1
  subtype3          6         22         11       15        11         0
  subtype4          5         22         18       24         1         0
D7V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          12       28       23       38
  STAGE IA          0        1        0        0
  STAGE II          5        9        8       13
  STAGE IIA        44       41       30       53
  STAGE IIB         2        2        2        5
  STAGE IIC         0        1        2        0
  STAGE III         2        8        4       13
  STAGE IIIA        5        6        6        5
  STAGE IIIB       17       15       22       22
  STAGE IIIC       17        4       11       18
  STAGE IV         14        6       15       24
  STAGE IVA         6        7       11        1
  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       T0+T1  T2  T3  T4
  subtype1     1  13  94  20
  subtype2     4  28  87  11
  subtype3     6  27  91  16
  subtype4     9  36 132  16
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        1        4        6        9
  T2          13       28       27       36
  T3          94       87       91      132
  T4          20       11       16       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  64  32  31
  subtype2  85  30  16
  subtype3  77  39  22
  subtype4 111  45  37
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       64       85       77      111
  N1       32       30       39       45
  N2       31       16       22       37
[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  92  17   2   0  14
  subtype2  98  10   0   1  21
  subtype3  92  20   6   0  21
  subtype4 165  24   1   0   0
D7V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        92       98       92      165
  M1        17       10       20       24
  M1A        2        0        6        1
  M1B        0        1        0        0
  MX        14       21       21        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 54 74
  subtype2 58 73
  subtype3 64 77
  subtype4 99 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   74
  subtype2   58   73
  subtype3   64   77
  subtype4   99   94
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       54       58       64       99
  MALE         74       73       77       94
[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                   83                            17
  subtype2                   82                            20
  subtype3                   93                             2
  subtype4                  114                            17
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    25                              3
  subtype2                    20                              5
  subtype3                    46                              0
  subtype4                    53                              5
D7V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                 83       82       93      114
  COLON MUCINOUS ADENOCARCINOMA        17       20        2       17
  RECTAL ADENOCARCINOMA                25       20       46       53
  RECTAL MUCINOUS ADENOCARCINOMA        3        5        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"
D7V10, binary
          cls
clus         0   1
  subtype1   3 125
  subtype2   3 128
  subtype3   2 139
  subtype4   1 192
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  125
  subtype2    3  128
  subtype3    2  139
  subtype4    1  192
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        3        2        1
  YES      125      128      139      192
[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  93   1   3   9
  subtype2  88   1   2   9
  subtype3  79   2   9  10
  subtype4 166   1  21   0
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       93       88       79      166
  R1        1        1        2        1
  R2        3        2        9       21
  RX        9        9       10        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                                1     4                        11
  subtype2                                0     4                        15
  subtype3                                0     4                         9
  subtype4                                0     0                         4
          vv
clus       WHITE
  subtype1   104
  subtype2    72
  subtype3    99
  subtype4    19
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   4        4        4        0
  BLACK OR AFRICAN AMERICAN              11       15        9        4
  WHITE                                 104       72       99       19
[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  47  17
  subtype2  90  12
  subtype3  33  10
  subtype4  46  19
  subtype5  55  10
  subtype6  74  19
  subtype7 113  19
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      64      102       43       65       65       93      132 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      17       12       10       19       10       19       19 
$subtype1
TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5664 TCGA-A6-6654 TCGA-A6-6780 
       43.43        37.05        37.25        22.09        23.87        20.12 
TCGA-AA-3655 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
       61.02        38.07         0.07         0.72         1.58         0.76 
TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-5403 
        0.20        58.39         1.41        32.94        65.00        62.79 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
      100.01         5.23         3.19         0.33         0.10        21.01 
TCGA-CM-5348 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-D5-5539 
       22.98        15.02        12.00        14.99        12.99        19.59 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6928 TCGA-DM-A28G 
       20.19         7.92        15.58         9.44        11.64        60.79 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       16.31        16.24         1.28        82.39        74.56        43.07 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       39.42        35.93        91.79        47.15        52.80         5.06 
TCGA-AF-3911 TCGA-AF-6655 TCGA-BM-6198 TCGA-DC-6158 TCGA-DT-5265 TCGA-EI-6917 
       37.74        20.02        10.19         7.10         5.29        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6814 
        8.45         9.96        14.86         0.53 

$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-A6-6650 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3495 TCGA-AA-3496 
       24.16        20.61        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-3660 
       35.01        58.03        62.96         6.97        19.07        78.08 
TCGA-AA-3662 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A01Z TCGA-AA-A02Y 
        6.05        37.05        85.05        19.04        37.02        39.98 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AY-5543 TCGA-AY-6386 
       21.37         4.21         0.79         0.10        15.75        17.82 
TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
        5.19        22.36        61.41         6.77        12.10        11.74 
TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 
        3.25        17.56        40.34        21.99         2.93       124.27 
TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6680 
       27.02        16.01        14.04        11.01        11.08        12.03 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D4 
       15.12        12.49        12.39        12.00       119.70        92.75 
TCGA-DM-A1D7 TCGA-DM-A280 TCGA-DM-A28M TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6293 
       13.32         7.76        95.18        29.59        33.67       107.67 
TCGA-G4-6295 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
        8.35        53.62        44.68        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2693 
       26.04        13.78        26.99        17.29        14.76        19.10 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3902 
       14.50        15.39        10.39         1.02        32.98        32.02 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.49         1.45         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        9.37         4.73        13.97        10.98        11.01        15.02 
TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
       13.97        30.05        20.55        20.91        18.28        17.69 
TCGA-EI-6881 TCGA-EI-6884 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       16.41        10.78         1.02        18.28        55.76        26.43 

$subtype3
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-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4313 
        6.97        56.55         0.92        27.09        21.44        50.37 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4951 
        5.65         5.13        49.41         2.24         3.06        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6171 
       15.62        51.32        23.05        20.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6930 
       12.95        13.05        20.42        17.85        16.14         1.51 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A288 
       10.26        24.43        49.91         7.50       135.65        14.04 
TCGA-DM-A28K TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-EI-6507 
       98.24        19.43        51.75        35.80        26.17        19.96 
TCGA-EI-6882 
        8.61 

$subtype4
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6652 TCGA-A6-A5ZU TCGA-AA-A02K 
       32.91        29.19        32.71        24.69         9.63        14.01 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 
        0.20         0.43        14.50         1.94         2.14         0.07 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 
      102.44        48.20         5.03        15.02        15.02        21.99 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6532 
       11.01        14.99        12.26        13.51        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
        1.32         4.50        17.13        13.41        11.38        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 
      130.65        12.59       140.38        44.32       139.17         6.12 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6855 
       26.47        81.37       119.93        35.97       117.07        35.41 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       28.21        23.51        55.04        36.00        46.75         4.11 
TCGA-AF-5654 TCGA-AG-3742 TCGA-AH-6549 TCGA-AH-6897 TCGA-CL-5918 TCGA-DC-5869 
        8.45         0.99         0.20         4.60         7.99        12.99 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 
       12.00        36.00       126.44        41.36        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-F5-6861 
        0.49        17.00        15.85        16.34         1.12 

$subtype5
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       31.63        30.44        23.61        29.16        22.52        25.08 
TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-A01X 
       21.76        20.28        61.84        52.44         1.02        26.01 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
        1.02         0.46        29.56         3.29         0.26         1.35 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 
        2.01         8.02        22.03        30.08        17.03        29.03 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5541 
       16.04        13.02        15.02        11.08        10.06        11.51 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-F4-6459 
        7.53        10.13        12.43        14.30         9.04         8.61 
TCGA-F4-6460 TCGA-F4-6854 TCGA-G4-6303 TCGA-G4-6310 TCGA-AF-2687 TCGA-AF-2690 
       13.38         0.53        61.87        45.11        24.13        17.23 
TCGA-AG-4022 TCGA-AH-6644 TCGA-CL-5917 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 
        0.99         0.72        60.03        15.02        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6514 
       10.06        57.24       129.27        24.13         2.40        16.31 
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-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.66         0.69         0.76         0.46        47.08 

$subtype6
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-3808 
       46.65        43.76        23.38        42.28        45.60        33.34 
TCGA-A6-3809 TCGA-A6-4107 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       32.75        32.45        13.02         1.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3554 
        8.05         0.99        14.01        33.99        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 
       29.95        23.01        19.99        54.02         2.01         0.92 
TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       50.04        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 
        0.99         0.99        33.04         0.99         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 
       38.99        37.02        33.07        36.03        53.00        27.02 
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-3980 TCGA-AA-3994 TCGA-AA-A00A 
       24.00         2.01        25.02        27.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       19.00        30.02        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       34.98         0.99        12.00        31.00         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02O TCGA-AA-A02R 
       35.01        39.06        51.98         2.96         0.92        22.03 
TCGA-AA-A03F TCGA-CM-4746 TCGA-CM-4748 TCGA-DM-A1HA TCGA-AF-2691 TCGA-AF-3400 
       18.05        37.02        26.04       131.51        43.04        12.72 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       12.00        32.02         2.01        50.04        12.03         6.05 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A015 TCGA-AG-A020 
       36.95        13.02        20.98        13.94        36.03        10.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 
       61.97        41.00         0.69 

$subtype7
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       37.02        17.79        44.91        35.11        15.52        34.65 
TCGA-A6-3810 TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       36.53         5.03         1.02         1.02        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       36.03        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3667 
       12.99        21.01        24.00        13.94        19.99        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 
       47.01        15.02        19.00        35.05        25.02        17.98 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       36.95        14.93        17.03         0.99        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 
       31.07        31.07        30.05        17.03        24.03        18.05 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
       12.99         2.01        20.98        34.03        21.99        36.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00K 
       27.02        19.07         7.96        13.94        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-A01F TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02F 
       15.02        32.02        31.00         1.02        33.04        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
        2.01         5.03        41.00        40.96        16.31         0.95 
TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AF-2692 
       75.25        83.80         8.02        13.02        29.06        13.55 
TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       10.39        36.03         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3608 
       24.00         1.02        46.03        34.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
       19.99        19.99         7.99         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       19.99         1.02        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       17.03         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 
       51.98        49.97         1.94        38.96        38.04       117.11 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.10     0.92     0.07     0.26     0.69     0.95 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  100.01   124.27   135.65   140.38   129.27   131.51   117.11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   15.91    16.85    19.66    16.34    13.64    24.03    19.99 
[1] "0.1 - 100.0 (15.9)" "0.1 - 124.3 (16.9)" "0.9 - 135.7 (19.7)"
[4] "0.1 - 140.4 (16.3)" "0.3 - 129.3 (13.6)" "0.7 - 131.5 (24.0)"
[7] "0.9 - 117.1 (20.0)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 54 10
  subtype2 72 33
  subtype3 43  2
  subtype4 49 18
  subtype5 40 25
  subtype6 81 20
  subtype7 90 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   10
  subtype2   72   33
  subtype3   43    2
  subtype4   49   18
  subtype5   40   25
  subtype6   81   20
  subtype7   90   52
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  COLON        54       72       43       49       40       81       90
  RECTUM       10       33        2       18       25       20       52
[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       6        0        4        21         0         0         2
  subtype2      21        1        7        21         2         1         7
  subtype3       9        0        3        23         1         0         1
  subtype4      11        0        0        18         1         1         0
  subtype5       6        0        2        18         1         1         1
  subtype6      18        0       12        28         5         0         8
  subtype7      30        0        7        39         1         0         8
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3          8         10        4         4         0
  subtype2          7         17          3        9         7         0
  subtype3          0          2          3        1         1         1
  subtype4          5         12          6        5         5         0
  subtype5          2         12          6        5         7         0
  subtype6          1         10          8        9         1         0
  subtype7          4         15         14       26         0         0
D8V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           6       21        9       11        6       18       30
  STAGE IA          0        1        0        0        0        0        0
  STAGE II          4        7        3        0        2       12        7
  STAGE IIA        21       21       23       18       18       28       39
  STAGE IIB         0        2        1        1        1        5        1
  STAGE IIC         0        1        0        1        1        0        0
  STAGE III         2        7        1        0        1        8        8
  STAGE IIIA        3        7        0        5        2        1        4
  STAGE IIIB        8       17        2       12       12       10       15
  STAGE IIIC       10        3        3        6        6        8       14
  STAGE IV          4        9        1        5        5        9       26
  STAGE IVA         4        7        1        5        7        1        0
  STAGE IVB         0        0        1        0        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       T0+T1 T2 T3 T4
  subtype1     1  7 47  9
  subtype2     7 21 65 13
  subtype3     1  8 32  4
  subtype4     1 12 46  8
  subtype5     0  8 48  8
  subtype6     4 16 69 12
  subtype7     6 32 97  9
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1        1        7        1        1        0        4        6
  T2           7       21        8       12        8       16       32
  T3          47       65       32       46       48       69       97
  T4           9       13        4        8        8       12        9
[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 31 15 18
  subtype2 61 35 10
  subtype3 36  4  5
  subtype4 35 19 12
  subtype5 29 22 12
  subtype6 64 18 19
  subtype7 81 33 30
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       31       61       36       35       29       64       81
  N1       15       35        4       19       22       18       33
  N2       18       10        5       12       12       19       30
[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  44   7   0   0  10
  subtype2  71  12   1   0  23
  subtype3  36   2   0   1   5
  subtype4  45   8   2   0  11
  subtype5  45   7   5   0   7
  subtype6  90   9   1   0   0
  subtype7 116  26   0   0   0
D8V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0        44       71       36       45       45       90      116
  M1         7       12        2        8        7        9       26
  M1A        0        1        0        2        5        1        0
  M1B        0        0        1        0        0        0        0
  MX        10       23        5       11        7        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 21 43
  subtype2 48 59
  subtype3 23 22
  subtype4 32 35
  subtype5 30 35
  subtype6 53 48
  subtype7 68 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   43
  subtype2   48   59
  subtype3   23   22
  subtype4   32   35
  subtype5   30   35
  subtype6   53   48
  subtype7   68   76
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       21       48       23       32       30       53       68
  MALE         43       59       22       35       35       48       76
[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                   41                            13
  subtype2                   66                             6
  subtype3                   33                            10
  subtype4                   47                             2
  subtype5                   39                             1
  subtype6                   57                            23
  subtype7                   89                             1
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                     8                              2
  subtype2                    31                              2
  subtype3                     1                              1
  subtype4                    18                              0
  subtype5                    25                              0
  subtype6                    11                              7
  subtype7                    50                              1
D8V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 41       66       33       47       39
  COLON MUCINOUS ADENOCARCINOMA        13        6       10        2        1
  RECTAL ADENOCARCINOMA                 8       31        1       18       25
  RECTAL MUCINOUS ADENOCARCINOMA        2        2        1        0        0
                                clus
vv                               subtype6 subtype7
  COLON ADENOCARCINOMA                 57       89
  COLON MUCINOUS ADENOCARCINOMA        23        1
  RECTAL ADENOCARCINOMA                11       50
  RECTAL MUCINOUS ADENOCARCINOMA        7        1
[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   3  61
  subtype2   2 105
  subtype3   0  45
  subtype4   0  67
  subtype5   3  62
  subtype6   1 100
  subtype7   0 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   61
  subtype2    2  105
  subtype3    0   45
  subtype4    0   67
  subtype5    3   62
  subtype6    1  100
  subtype7    0  144
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         3        2        0        0        3        1        0
  YES       61      105       45       67       62      100      144
[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  45   0   0   5
  subtype2  64   2   3   6
  subtype3  28   1   0   5
  subtype4  36   0   2   7
  subtype5  47   0   0   5
  subtype6  88   0   7   0
  subtype7 118   2  23   0
D8V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       45       64       28       36       47       88      118
  R1        0        2        1        0        0        0        2
  R2        0        3        0        2        0        7       23
  RX        5        6        5        7        5        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                                1     3                         5
  subtype2                                0     1                        13
  subtype3                                0     3                         4
  subtype4                                0     2                         8
  subtype5                                0     3                         4
  subtype6                                0     0                         1
  subtype7                                0     0                         4
          vv
clus       WHITE
  subtype1    53
  subtype2    71
  subtype3    36
  subtype4    54
  subtype5    55
  subtype6    13
  subtype7    12
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        1        3        2        3
  BLACK OR AFRICAN AMERICAN               5       13        4        8        4
  WHITE                                  53       71       36       54       55
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        0
  BLACK OR AFRICAN AMERICAN               1        4
  WHITE                                  13       12
[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 166  39
  subtype2  73  22
  subtype3 180  40
subtype1 subtype2 subtype3 
     205       95      220 
subtype1 subtype2 subtype3 
      39       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        21.01         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        66         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         10         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        66       26       61
  STAGE IIB         4        0        6
  STAGE IIC         2        0        0
  STAGE III         8        3       16
  STAGE IIIA       10        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       T0+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
  T0+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 176  47
  subtype2 110  25
  subtype3 133  29
subtype1 subtype2 subtype3 
     223      135      162 
subtype1 subtype2 subtype3 
      47       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        21.01         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        77         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          9         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        77       34       42
  STAGE IIB         4        2        4
  STAGE IIC         1        1        0
  STAGE III         8        7       12
  STAGE IIIA        9        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       T0+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
  T0+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 75 20
  subtype2 90 17
  subtype3 66 19
subtype1 subtype2 subtype3 
      95      107       85 
subtype1 subtype2 subtype3 
      20       17       19 
$subtype1
TCGA-A6-2675 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 
       43.43        30.44        29.19        27.09        24.13        20.61 
TCGA-AA-3511 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3697 TCGA-AD-6890 TCGA-AD-6965 
        6.97        78.08         6.05        85.05         0.79         0.20 
TCGA-AU-3779 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       14.50        29.56         1.94         0.07         0.26         1.35 
TCGA-CK-5912 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6170 
       48.20        16.01         5.03        15.02        15.02        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.08        11.01        14.99        12.26        13.51        11.51 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 
       18.25         1.32        17.13        15.58        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38       119.70        38.20       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6307 TCGA-G4-6317 
      117.07        33.67       107.67        28.21        55.04        36.00 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3742 TCGA-AH-6549 
       37.74         8.45        20.02        10.39         0.99         0.20 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.69         6.05         6.05         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00         7.10        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 TCGA-G5-6641 
       20.55        20.91        17.00        16.34        26.43 

$subtype2
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 
       14.53        33.53        22.06        32.71         8.38        25.18 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3655 TCGA-AA-3663 
       24.39        20.12        19.66         1.02        61.02         6.97 
TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       19.04         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.10         0.92        27.09        15.75        21.44        17.82 
TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       11.74         2.24         3.25         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        15.62        51.32        21.99        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
      124.27        23.05        27.02        15.02        15.02        12.00 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6529 
       14.04        11.01        12.95        13.05        12.03        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       20.42        17.75        15.12         4.50        12.49        16.14 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD 
       12.39         9.44        11.64        12.00        10.26        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K 
       92.75        49.91       135.65         7.76        14.04        98.24 
TCGA-DM-A28M TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6299 
       95.18         6.18        29.59        19.43         8.35        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6136 TCGA-AG-3732 TCGA-AH-6544 
       46.75        52.80        19.10        15.39        32.98         0.49 
TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6507 
        1.45        10.19         4.73        13.97        30.05        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-G5-6233 TCGA-G5-6235 
       18.28        15.85        17.69        18.28        55.76 

$subtype3
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 
       32.91        31.63        23.61        22.09        29.16        22.52 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        24.16        21.76        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AY-6196 
        1.02         1.58         1.02         0.76         0.46         0.20 
TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5797 
        1.41        62.79         5.23         3.19         3.06         3.29 
TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5868 
        0.33         2.01        22.03        22.98        30.08        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6536 
       13.02        11.08        10.06        19.59         7.92        17.85 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6460 
        7.53        10.13         1.51         6.12         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.64        13.45        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6298 
       16.24         1.28         0.53        35.41        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6627 TCGA-AF-2687 
       43.07        61.87        45.11        35.93        47.15        24.13 
TCGA-AF-2690 TCGA-AF-4110 TCGA-AG-3731 TCGA-AG-4022 TCGA-AH-6644 TCGA-DC-6681 
       17.23        14.50         1.02         0.99         0.72        12.95 
TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 
        5.29       129.27        24.13        16.31         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-G5-6572 
       47.08 

subtype1 subtype2 subtype3 
    0.07     0.07     0.20 
subtype1 subtype2 subtype3 
  140.38   135.65   129.27 
subtype1 subtype2 subtype3 
   15.02    18.28    14.86 
[1] "0.1 - 140.4 (15.0)" "0.1 - 135.7 (18.3)" "0.2 - 129.3 (14.9)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 62 39
  subtype2 93 15
  subtype3 65 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   39
  subtype2   93   15
  subtype3   65   19
        clus
vv       subtype1 subtype2 subtype3
  COLON        62       93       65
  RECTUM       39       15       19
[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      16        0        2        29         2         0         4
  subtype2      19        1        6        34         2         2         5
  subtype3       6        0        4        27         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         14         11        6         5         0
  subtype2          4         18          4        5         4         1
  subtype3          2         12         12        8         9         0
D11V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          16       19        6
  STAGE IA          0        1        0
  STAGE II          2        6        4
  STAGE IIA        29       34       27
  STAGE IIB         2        2        1
  STAGE IIC         0        2        0
  STAGE III         4        5        0
  STAGE IIIA        7        4        2
  STAGE IIIB       14       18       12
  STAGE IIIC       11        4       12
  STAGE IV          6        5        8
  STAGE IVA         5        4        9
  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       T0+T1 T2 T3 T4
  subtype1     6 16 69 10
  subtype2     2 22 75  9
  subtype3     1  5 64 14
D11V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        6        2        1
  T2          16       22        5
  T3          69       75       64
  T4          10        9       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 53 28 19
  subtype2 69 30  9
  subtype3 40 20 23
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       53       69       40
  N1       28       30       20
  N2       19        9       23
[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 76  7   3   0 14
  subtype2 73  7   1   1 25
  subtype3 55 13   3   0 11
D11V7, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        76       73       55
  M1         7        7       13
  M1A        3        1        3
  M1B        0        1        0
  MX        14       25       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"
D11V8, binary
          cls
clus        0  1
  subtype1 42 59
  subtype2 49 60
  subtype3 39 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   59
  subtype2   49   60
  subtype3   39   46
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42       49       39
  MALE         59       60       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       COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  subtype1                   61                             1
  subtype2                   76                            17
  subtype3                   54                            11
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    38                              1
  subtype2                    15                              0
  subtype3                    18                              1
D11V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                 61       76       54
  COLON MUCINOUS ADENOCARCINOMA         1       17       11
  RECTAL ADENOCARCINOMA                38       15       18
  RECTAL MUCINOUS ADENOCARCINOMA        1        0        1
[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"
D11V10, binary
          cls
clus         0   1
  subtype1   3  98
  subtype2   2 107
  subtype3   2  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   98
  subtype2    2  107
  subtype3    2   83
     clus
vv    subtype1 subtype2 subtype3
  NO         3        2        2
  YES       98      107       83
[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 54  0  2  9
  subtype2 64  2  1 11
  subtype3 57  0  1  4
D11V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       54       64       57
  R1        0        2        0
  R2        2        1        1
  RX        9       11        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"
D11V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         4
  subtype2                                0     4                         9
  subtype3                                1     4                         7
          vv
clus       WHITE
  subtype1    83
  subtype2    91
  subtype3    70
D11V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        4        4
  BLACK OR AFRICAN AMERICAN               4        9        7
  WHITE                                  83       91       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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 62 17
  subtype2 38 13
  subtype3 54 13
  subtype4 27  4
  subtype5 50  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      79       51       67       31       59 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       13       13        4        9 
$subtype1
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-AA-3511 
       43.43        27.09        24.13        25.18        20.61         6.97 
TCGA-AA-3655 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5821 TCGA-AU-3779 
       61.02         4.21         0.79         0.10         0.92        14.50 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-AZ-6608 
       15.75        17.82        61.41        49.41        11.74         1.94 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-6747 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6170 
       17.56        40.34         2.93        22.03        14.04        15.02 
TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-5537 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 
       11.08        11.08        14.99        15.12         4.50        12.49 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 
       15.58        12.39        12.43       119.70        24.43        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28C 
       13.32        12.59       140.38         7.50        44.32        81.37 
TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6293 
      119.93       117.07        98.24        29.59        33.67       107.67 
TCGA-G4-6294 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       28.21        53.62        44.68        36.00        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 
       13.78        91.79        46.75        19.10        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3732 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-BM-6198 
       10.39        32.98         0.49         1.45         0.69        10.19 
TCGA-CI-6622 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-6155 TCGA-DY-A0XA TCGA-DY-A1DC 
        6.97         9.37        11.01        13.97       126.44        41.36 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 TCGA-G5-6233 
       51.48        32.61         2.40        15.85        17.69        18.28 
TCGA-G5-6235 
       55.76 

$subtype2
TCGA-A6-4105 TCGA-A6-5666 TCGA-A6-6142 TCGA-AA-3496 TCGA-AA-3660 TCGA-AA-3662 
       14.53        32.71        25.08         1.02        78.08         6.05 
TCGA-AA-3697 TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-6965 TCGA-AZ-6599 
       85.05        21.37         1.58         0.76         0.20         6.77 
TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
        3.29       102.44        48.20        22.98        16.01         5.03 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5538 TCGA-D5-5541 
       15.02        29.03        13.02        11.01        12.26        11.51 
TCGA-D5-6532 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F 
       18.25       130.65       131.51         6.12        26.47        35.97 
TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6322 TCGA-AG-3731 TCGA-AG-3742 
       82.39        55.04        39.42        26.04         1.02         0.99 
TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.20         6.05         6.05         4.73        60.03         7.99 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A1DD TCGA-EI-6508 TCGA-EI-6513 
       15.02        36.00         7.10        57.24        20.91        16.34 
TCGA-F5-6702 TCGA-G5-6572 TCGA-G5-6641 
       14.86        47.08        26.43 

$subtype3
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 
       32.91        31.63        30.44        23.61        29.16        22.52 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         1.02 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6603 
        1.02         0.46         0.20         1.41        62.79        29.56 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5868 
        5.23         0.33         1.35         2.01        30.08        17.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 
       16.04        14.99        12.99        11.01        10.06        19.59 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 
       17.75         7.92         7.53        10.13         9.04        11.38 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
        8.61        11.11        13.45         1.55        16.31        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 
        1.28         0.53        35.41        43.07        61.87        45.11 
TCGA-G4-6627 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6644 
       47.15        17.23        37.74        14.50         0.99         0.72 
TCGA-DC-4745 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6509 
       10.98        12.95        10.06       129.27        24.13        17.00 
TCGA-EI-6514 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       16.31         9.96        37.51        31.30         1.02         0.66 
TCGA-F5-6813 
        0.69 

$subtype4
TCGA-A6-5660 TCGA-A6-5664 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-6161 
       29.19        22.09         0.07         0.26        21.99        15.02 
TCGA-CM-6166 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
       21.99        13.51         1.32        17.13        14.30        13.41 
TCGA-DM-A0XF TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 
       38.20       139.17        60.79        13.38        13.64         8.35 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6315 TCGA-AF-2687 TCGA-AF-5654 TCGA-CL-4957 
       23.51        35.93        36.72        24.13         8.45        13.97 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6682 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 
       15.02        12.99        13.05         0.49        20.55        18.28 
TCGA-F5-6810 
        0.39 

$subtype5
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       33.53        22.06         8.38        24.39        20.12        19.66 
TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 
        6.97        19.04         0.07        56.55         0.72        27.09 
TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5254 
       21.44         5.13        12.10       100.01         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        3.06         3.25         0.10        15.62        51.32        21.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
      124.27        23.05        27.02        15.02        15.02        12.00 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       14.04        12.95        13.05        12.03        20.19        20.42 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       17.85        16.14         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28M 
       10.26        49.91       135.65         7.76        14.04        95.18 
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-DC-6160 TCGA-DT-5265 TCGA-EI-6507 
       26.17        52.80        30.05         5.29        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.20     0.20     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  140.38   131.51   129.27   139.17   135.65 
subtype1 subtype2 subtype3 subtype4 subtype5 
   17.82    16.01    14.99    15.02    17.85 
[1] "0.1 - 140.4 (17.8)" "0.2 - 131.5 (16.0)" "0.2 - 129.3 (15.0)"
[4] "0.1 - 139.2 (15.0)" "0.1 - 135.7 (17.9)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 57 24
  subtype2 35 18
  subtype3 49 17
  subtype4 22 11
  subtype5 57  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   24
  subtype2   35   18
  subtype3   49   17
  subtype4   22   11
  subtype5   57    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  COLON        57       35       49       22       57
  RECTUM       24       18       17       11        3
[1] 2 5
[1] 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      11        1        3        26         2         1         4
  subtype2       8        0        2         8         0         1         3
  subtype3       5        0        3        20         1         0         0
  subtype4       5        0        1         9         1         0         1
  subtype5      12        0        3        27         1         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          7         11          4        3         4         0
  subtype2          2         10          4        6         5         0
  subtype3          3         10         11        3         8         0
  subtype4          1          7          4        3         1         0
  subtype5          0          6          4        4         0         1
D12V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          11        8        5        5       12
  STAGE IA          1        0        0        0        0
  STAGE II          3        2        3        1        3
  STAGE IIA        26        8       20        9       27
  STAGE IIB         2        0        1        1        1
  STAGE IIC         1        1        0        0        0
  STAGE III         4        3        0        1        1
  STAGE IIIA        7        2        3        1        0
  STAGE IIIB       11       10       10        7        6
  STAGE IIIC        4        4       11        4        4
  STAGE IV          3        6        3        3        4
  STAGE IVA         4        5        8        1        0
  STAGE IVB         0        0        0        0        1
[1] 13  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     5 14 56  6
  subtype2     2  7 37  6
  subtype3     0  6 50 11
  subtype4     1  5 23  4
  subtype5     1 11 42  6
D12V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        5        2        0        1        1
  T2          14        7        6        5       11
  T3          56       37       50       23       42
  T4           6        6       11        4        6
[1] 4 5
[1] TRUE
[1] "dimension 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 49 24  8
  subtype2 20 19 12
  subtype3 31 18 17
  subtype4 18  9  6
  subtype5 44  8  8
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       49       20       31       18       44
  N1       24       19       18        9        8
  N2        8       12       17        6        8
[1] 3 5
[1] 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 57  5   1   0 17
  subtype2 30  8   3   0 10
  subtype3 46  7   3   0 10
  subtype4 24  3   0   0  6
  subtype5 47  4   0   1  7
D12V7, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        57       30       46       24       47
  M1         5        8        7        3        4
  M1A        1        3        3        0        0
  M1B        0        0        0        0        1
  MX        17       10       10        6        7
[1] 5 5
[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 39 43
  subtype2 21 32
  subtype3 33 34
  subtype4 15 18
  subtype5 22 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   43
  subtype2   21   32
  subtype3   33   34
  subtype4   15   18
  subtype5   22   38
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       39       21       33       15       22
  MALE         43       32       34       18       38
[1] 2 5
[1] 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                             1
  subtype2                   32                             3
  subtype3                   42                             7
  subtype4                   20                             2
  subtype5                   41                            16
          vv
clus       RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  subtype1                    24                              0
  subtype2                    17                              1
  subtype3                    17                              0
  subtype4                    11                              0
  subtype5                     2                              1
D12V9, multiclass
                                clus
vv                               subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                 56       32       42       20       41
  COLON MUCINOUS ADENOCARCINOMA         1        3        7        2       16
  RECTAL ADENOCARCINOMA                24       17       17       11        2
  RECTAL MUCINOUS ADENOCARCINOMA        0        1        0        0        1
[1] 4 5
[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  3 79
  subtype2  0 53
  subtype3  3 64
  subtype4  1 32
  subtype5  0 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   79
  subtype2    0   53
  subtype3    3   64
  subtype4    1   32
  subtype5    0   60
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         3        0        3        1        0
  YES       79       53       64       32       60
[1] 2 5
[1] 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  2  0  4
  subtype2 29  0  3  4
  subtype3 46  0  0  3
  subtype4 21  0  0  4
  subtype5 36  0  1  9
D12V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       43       29       46       21       36
  R1        2        0        0        0        0
  R2        0        3        0        0        1
  RX        4        4        3        4        9
[1] 4 5
[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                                0     0                         5
  subtype2                                0     1                         2
  subtype3                                1     2                         4
  subtype4                                0     2                         4
  subtype5                                0     6                         5
          vv
clus       WHITE
  subtype1    71
  subtype2    42
  subtype3    58
  subtype4    26
  subtype5    47
D12V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        1        2        2        6
  BLACK OR AFRICAN AMERICAN               5        2        4        4        5
  WHITE                                  71       42       58       26       47
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
