[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"        "-oTCOAD-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/COAD-TP/11541421/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/11590519/COAD-TP.mergedcluster.txt"

nPatients in clinical file=449, in cluster file=459, common to both=448
[1]  12 448
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
38 61 30 24 
 1  2  3  4 
38 61 30 24 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
46 73 34 
 1  2  3 
46 73 34 
[1] "CN_CNMF"
[1] 3
  1   2   3 
201 174  64 
  1   2   3 
201 174  64 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
115  92  71 
  1   2   3 
115  92  71 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
 80 128  27  96 
  1   2   3   4 
 80 128  27  96 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
60 49 56 68 69 29 
 1  2  3  4  5  6 
60 49 56 68 69 29 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
139 151 148 
  1   2   3 
139 151 148 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
104  74  89 132  39 
  1   2   3   4   5 
104  74  89 132  39 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
160  66 180 
  1   2   3 
160  66 180 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
136  50  79 141 
  1   2   3   4 
136  50  79 141 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
29 32 24 
 1  2  3 
29 32 24 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
12 22 17 24 10 
 1  2  3  4  5 
12 22 17 24 10 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 448 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
         154          160         1126         1419         1331         1321 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
         711          541         1286         1366         1068         1387 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
          NA          472         1127         1133          488         1054 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
        1014          996         1111           NA          987         1001 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
         962          926          888         1020          718          672 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
         671          995          887          824          685          734 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
         255          763          766          735          627          662 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
         751          742          726          612          598          617 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
          NA           NA           NA         1595          293           NA 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
          31           NA           31         1127           31         1065 
TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1765         1915         1946          212           31           NA 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 
        1186           31          276          731           NA         1127 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 
        1096          245          580           NA           NA          580 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        1035          882          882          791          395           30 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
         426         1034          639           NA          730          546 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
         911          700          638          608          424          608 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
        1856         2375          184          212         1643           NA 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
         426           28         1522         1431         1430          457 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
          NA          182           NA         1127          578           NA 
TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 
          NA           NA           NA         2587          821           NA 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3815 
         579           30           30         1066           NA         1005 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
          NA          761           31          547          485         1186 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
        1124         1126          454           NA          518           30 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
          NA         1006           NA         1096          975           30 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 
         945          945           NA          914         1612          518 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 
         731           NA          912           NA          549          943 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
          NA          395          730         1004          791          730 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 
          NA          638         1035           61          669         1096 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
         489         1551          397         1036          791          761 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 
         730          822          822           NA          580           NA 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
         822          424         1157          578          913         1035 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
         549          549          518           NA          822         1278 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
          30          518          456          669         1064          457 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
         457           30          974          365          943          943 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
          NA           31         1065           31         1005         1065 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
         791         1126           NA           NA         1581           NA 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R 
        1216           NA           NA           NA           28           NA 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        1247         1216           NA         1246            2          650 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
         128         1720           24           22           48           31 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 
           3           23            6           NA           13           14 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
          28          441          824           NA           NA          479 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
           6          652          542          158          168          209 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        2289         1532         1776           NA           NA         1002 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
          NA         2549           NA         1977           NA         1868 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
          NA           NA           NA           68           93           65 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
          99          100            2            8           10            3 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
          41          534         3116         1227         2134          475 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 
        1466         1561          669           NA           NA           NA 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
          89           61         3780          701          609         1126 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
         244          792          244          822          396          884 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
         670          699          915          487          457           NA 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
         457          457          518          457          365          427 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
         883          488          669          456          395          396 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
         457          427          335          394          397          337 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
         337          335          306          366          456          373 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
         596          411          350          614          621          540 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
         555           40          241          460          543          137 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
         521          380          491          474          229          377 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
         308          378          435          275          287          354 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
         408           46          365          346          312         3641 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
         743         1162         3974         2821         1518          405 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
         383         4270          228         1348         4000         4126 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
         236         4233          186          427          805         2475 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
        3648         1094         1849         3561         2988         2895 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
          NA          407           NA          415          409           NA 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        1091           47          496          900          494         1024 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
          39           16         1077          591         3275           NA 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
         254         2506           NA         2268         1310         1882 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
        1631         1359         1674         1574         1372         1199 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
        1093         1117         1095          804          672          792 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
         419         1089          796         2792           NA         1434 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
        1606          125           NA          320           85          182 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
         170           40          158          167          821          526 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
         202          449          921         2038 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=80,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=284,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	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=21,	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=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 448 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  77 306  53 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  77 306  53 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  77 306  53 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  77 306  53 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
264 103  80 
[1] "table(vv)"
vv
 N0  N1  N2 
264 103  80 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
264 103  80 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
264 103  80 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, 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=21, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 27  7
  subtype2 44 12
  subtype3 24  4
  subtype4 20  3
subtype1 subtype2 subtype3 subtype4 
      34       56       28       23 
subtype1 subtype2 subtype3 subtype4 
       7       12        4        3 
$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-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3672 
        1.02        13.02         0.99        17.95        29.95         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-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       24.00         2.01        25.02        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A02R 
       18.05         0.99         0.99        22.03 

$subtype2
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3517 TCGA-AA-3519 
       17.79        42.28        15.52        34.65        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       36.03        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 
       33.99        21.01        24.00        19.99        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3837 
       14.01        15.02        19.00         5.03        35.05        38.99 
TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3869 
       36.95         0.99        31.07        31.07        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       18.05         2.01        20.98        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L 
       34.06        26.01        24.00         7.96        34.03        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        14.99        21.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       32.02        31.00         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AY-4070 
       41.00        16.31 

$subtype3
TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3556 
        1.02        37.05         8.05        19.07        14.01        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-3818 TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3994 
        0.99         1.02        36.03        53.00        24.00        27.02 
TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01G 
       13.94        18.05         4.01        17.03        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01Q TCGA-AA-A024 TCGA-AA-A029 
       31.00         1.02        39.06        51.98 

$subtype4
TCGA-AA-3520 TCGA-AA-3532 TCGA-AA-3552 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       24.03        29.00        13.02        50.04        47.01        37.05 
TCGA-AA-3692 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 
       36.00        25.02        17.98        14.93        17.03        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3862 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3970 
       32.05         0.99        30.05        12.99        34.03        36.03 
TCGA-AA-3971 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AY-4071 
       16.08        27.02        27.02        19.07         0.95 

subtype1 subtype2 subtype3 subtype4 
    0.92     0.99     0.99     0.95 
subtype1 subtype2 subtype3 subtype4 
   46.65    50.99    54.02    50.04 
subtype1 subtype2 subtype3 subtype4 
   23.69    21.99    18.56    27.02 
[1] "0.9 - 46.6 (23.7)" "1.0 - 51.0 (22.0)" "1.0 - 54.0 (18.6)"
[4] "0.9 - 50.0 (27.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       6        1        14         3         3          1          3
  subtype2      11        2        12         0         2          2          5
  subtype3       7        6         9         2         1          0          3
  subtype4       5        3        10         0         2          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        5         0
  subtype2         13       14         0
  subtype3          0        1         1
  subtype4          2        1         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           6       11        7        5
  STAGE II          1        2        6        3
  STAGE IIA        14       12        9       10
  STAGE IIB         3        0        2        0
  STAGE III         3        2        1        2
  STAGE IIIA        1        2        0        0
  STAGE IIIB        3        5        3        1
  STAGE IIIC        1       13        0        2
  STAGE IV          5       14        1        1
  STAGE IVA         0        0        1        0
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  7 24  6
  subtype2  2 12 42  5
  subtype3  0  7 19  4
  subtype4  1  5 18  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        2        0        1
  T2        7       12        7        5
  T3       24       42       19       18
  T4        6        5        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"
          vv
clus       N0 N1 N2
  subtype1 25  5  8
  subtype2 27 15 19
  subtype3 24  5  1
  subtype4 18  3  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       25       27       24       18
  N1        5       15        5        3
  N2        8       19        1        3
[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 32  5   0
  subtype2 47 14   0
  subtype3 28  1   1
  subtype4 22  1   0
D1V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        32       47       28       22
  M1         5       14        1        1
  M1A        0        0        1        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"
D1V7, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 31 30
  subtype3 10 20
  subtype4  9 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   31   30
  subtype3   10   20
  subtype4    9   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       31       10        9
  MALE         13       30       20       15
[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"
D1V8, binary
          cls
clus        0  1
  subtype1 25 13
  subtype2 60  1
  subtype3 22  7
  subtype4 22  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   13
  subtype2   60    1
  subtype3   22    7
  subtype4   22    1
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                25       60       22       22
  COLON MUCINOUS ADENOCARCINOMA       13        1        7        1
[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"
D1V9, binary
          cls
clus        0
  subtype1 38
  subtype2 61
  subtype3 30
  subtype4 24
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 R1 R2
  subtype1 32  0  3
  subtype2 47  1 13
  subtype3 28  0  2
  subtype4 21  0  1
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       32       47       28       21
  R1        0        1        0        0
  R2        3       13        2        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"
D1V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     6
  subtype2                         1     4
  subtype3                         0     0
  subtype4                         0     1
D1V12, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype4 
       6        5        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
                           clus
vv                          subtype1 subtype2
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            6        4
[1] 2 2
[1] FALSE

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 34  8
  subtype2 54 15
  subtype3 27  3
subtype1 subtype2 subtype3 
      42       69       30 
subtype1 subtype2 subtype3 
       8       15        3 
$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-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
        2.01        25.02        27.02        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 

$subtype2
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3519 
       17.79        42.28        15.52        34.65        36.53         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
       24.03        37.05        36.03        19.07        34.03        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       14.01        33.99        21.01        20.98        19.99        13.94 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       54.02         2.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
        5.98        36.00         5.03         0.99        25.02        17.98 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3869 
       38.99        14.93         0.99        33.07        32.05        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
       18.05        12.99        24.00        50.99        13.05        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       24.00        19.07         7.96        13.94        19.00        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       17.03        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       31.00        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AY-4070 
        5.03        41.00        16.31 

$subtype3
TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 
       38.99        29.00        26.01        12.99        13.02        24.00 
TCGA-AA-3562 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3812 
       19.99        14.01        15.02        37.05        19.00        35.05 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 
       36.95        17.03         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       17.03        24.03         2.01        20.98        34.03        21.99 
TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4071 
       36.03        16.08        34.06        27.02        34.03         0.95 

subtype1 subtype2 subtype3 
    0.92     0.99     0.95 
subtype1 subtype2 subtype3 
   53.00    54.02    38.99 
subtype1 subtype2 subtype3 
  23.195   21.010   24.015 
[1] "0.9 - 53.0 (23.2)" "1.0 - 54.0 (21.0)" "0.9 - 39.0 (24.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  subtype1       9        3        14         4         3          1          5
  subtype2      12        7        20         1         4          2          4
  subtype3       8        2        11         0         1          0          3
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        5         0
  subtype2         10       12         1
  subtype3          5        4         0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9       12        8
  STAGE II          3        7        2
  STAGE IIA        14       20       11
  STAGE IIB         4        1        0
  STAGE III         3        4        1
  STAGE IIIA        1        2        0
  STAGE IIIB        5        4        3
  STAGE IIIC        1       10        5
  STAGE IV          5       12        4
  STAGE IVA         0        1        0
[1] 10  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 10 28  7
  subtype2  2 13 51  7
  subtype3  1  8 24  1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        2        1
  T2       10       13        8
  T3       28       51       24
  T4        7        7        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"
          vv
clus       N0 N1 N2
  subtype1 31  7  8
  subtype2 42 16 15
  subtype3 21  5  8
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       31       42       21
  N1        7       16        5
  N2        8       15        8
[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
  subtype1 40  5   0
  subtype2 60 12   1
  subtype3 29  4   0
D2V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        40       60       29
  M1         5       12        4
  M1A        0        1        0
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 28 18
  subtype2 35 38
  subtype3 12 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   18
  subtype2   35   38
  subtype3   12   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       35       12
  MALE         18       38       22
[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"
D2V8, binary
          cls
clus        0  1
  subtype1 27 18
  subtype2 69  4
  subtype3 33  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   18
  subtype2   69    4
  subtype3   33    0
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                27       69       33
  COLON MUCINOUS ADENOCARCINOMA       18        4        0
[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"
D2V9, binary
          cls
clus        0
  subtype1 46
  subtype2 73
  subtype3 34
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 R1 R2
  subtype1 39  0  3
  subtype2 60  1 12
  subtype3 29  0  4
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       39       60       29
  R1        0        1        0
  R2        3       12        4
[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"
D2V11, continuous
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         0     5
  subtype2                         1     5
  subtype3                         0     1
D2V12, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       5        6        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
                           clus
vv                          subtype1 subtype2
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            5        5
[1] 2 2
[1] FALSE

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 151  40
  subtype2 134  34
  subtype3  50  13
subtype1 subtype2 subtype3 
     191      168       63 
subtype1 subtype2 subtype3 
      40       34       13 
$subtype1
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 
        5.06        46.65        43.76        23.38        42.28        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       37.05        37.25        16.04        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.06         8.38        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         1.02         3.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 
       24.03        37.05         8.05        19.07        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 
       17.95        29.95        61.02         6.97         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       11.01        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       36.03        32.05        53.00        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 
       12.99        33.01        26.01        24.00         2.01         2.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       25.02        19.07        27.02        38.04        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01I 
        4.01        27.02         0.99        34.98         0.99        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       39.06        51.98        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-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        32.94         5.13        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 
       12.10       100.01         3.19         3.06         3.25         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       37.02        26.04        15.02        15.02        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       14.99        12.99        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       12.03        20.19        20.42        17.75         7.92        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.49        16.14        12.39        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 
       13.41         1.51        12.00        10.26        24.43        49.91 
TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G 
       13.32       135.65         7.76       139.17        81.37        60.79 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 
       35.87         1.55        29.59        16.24        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      107.67        23.51        43.07        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       52.80         2.79         5.98        14.76        67.00 

$subtype2
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       15.52        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       30.44        29.19        23.61        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 
       24.13        25.08        20.61        24.69        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-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       23.01        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3841 
       50.04        15.02        37.05        19.00        85.05        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        33.07         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       31.07        17.03        27.02        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00L 
       24.00        27.02         7.96        13.94        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       32.02        12.00        33.04         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96         4.21         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.43        14.50        16.31         0.95        15.75 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-4684 
        5.19         5.52         6.87        75.25        22.36        65.00 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 
       29.56         5.23         1.94         2.14         0.07         1.35 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       48.20        21.99         2.01         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        16.01         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6677 
       14.04        29.03        16.04        21.99        15.02        11.08 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 
       10.06        14.99        19.59        13.51        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6922 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
       15.12        17.13        10.13        11.38       130.65        92.75 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       12.59       140.38       131.51        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.97         8.61        13.38        33.67         1.28         0.53 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       28.21         8.35        82.39        61.87        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       39.42        35.93        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        4.11        10.52         1.32         5.19         5.49        26.99 

$subtype3
TCGA-4T-AA8H TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 
        5.26        27.09        25.18         9.63         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3553 TCGA-AA-3558 
        1.02        36.03        19.07        26.01        24.00        20.98 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3692 
       78.08         6.05        54.02        47.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-A00D TCGA-AA-A00K 
        5.03        31.07        24.03        29.98        19.00        18.05 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O TCGA-AY-6197 TCGA-AZ-4614 
        1.02        37.02         5.03         0.92        21.44         5.65 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5797 TCGA-CK-4952 
       83.80        62.79        11.74         2.24         3.29        15.62 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 
       27.02        22.98        30.08        13.02        11.01        11.08 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 
       12.26        11.51         4.50        15.58         7.53        12.43 
TCGA-D5-6926 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 
        9.04       119.70        38.20         7.50        44.32         6.12 
TCGA-DM-A28H TCGA-F4-6805 TCGA-G4-6299 TCGA-G4-6306 TCGA-NH-A50U TCGA-NH-A6GB 
      117.07        16.31        74.56        44.68        10.98         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       17.29         6.64        30.28 

subtype1 subtype2 subtype3 
    0.07     0.07     0.92 
subtype1 subtype2 subtype3 
  139.17   140.38   119.70 
subtype1 subtype2 subtype3 
   20.12    19.99    17.29 
[1] "0.1 - 139.2 (20.1)" "0.1 - 140.4 (20.0)" "0.9 - 119.7 (17.3)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      40        1       15        72         6         0        10
  subtype2      22        0        6        45         2         1         7
  subtype3      10        0        7        14         0         0         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         21         14       11         3         1
  subtype2          8         24         18       23        12         1
  subtype3          1         10          6        9         3         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          40       22       10
  STAGE IA          1        0        0
  STAGE II         15        6        7
  STAGE IIA        72       45       14
  STAGE IIB         6        2        0
  STAGE IIC         0        1        0
  STAGE III        10        7        4
  STAGE IIIA        3        8        1
  STAGE IIIB       21       24       10
  STAGE IIIC       14       18        6
  STAGE IV         11       23        9
  STAGE IVA         3       12        3
  STAGE IVB         1        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   6  38 130  26
  subtype2   5  26 124  19
  subtype3   0  12  46   6
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        6        5        0
  T2       38       26       12
  T3      130      124       46
  T4       26       19        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1 138  35  28
  subtype2  83  53  37
  subtype3  35  15  14
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      138       83       35
  N1       35       53       15
  N2       28       37       14
[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 159  12   1   1  25
  subtype2 117  30   5   1  18
  subtype3  44  10   2   0   7
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       159      117       44
  M1        12       30       10
  M1A        1        5        2
  M1B        1        1        0
  MX        25       18        7
[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"
D3V7, binary
          cls
clus         0   1
  subtype1 102  99
  subtype2  75  99
  subtype3  30  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102   99
  subtype2   75   99
  subtype3   30   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      102       75       30
  MALE         99       99       34
[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"
D3V8, binary
          cls
clus         0   1
  subtype1 154  47
  subtype2 166   6
  subtype3  58   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  154   47
  subtype2  166    6
  subtype3   58    6
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               154      166       58
  COLON MUCINOUS ADENOCARCINOMA       47        6        6
[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"
D3V9, binary
          cls
clus         0   1
  subtype1   0 201
  subtype2   2 172
  subtype3   1  63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  201
  subtype2    2  172
  subtype3    1   63
     clus
vv    subtype1 subtype2 subtype3
  NO         0        2        1
  YES      201      172       63
[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 147   2   4  15
  subtype2 122   1  13   7
  subtype3  44   0   7   3
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      147      122       44
  R1        2        1        0
  R2        4       13        7
  RX       15        7        3
[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"
D3V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                        23
  subtype2                                0     3                        19
  subtype3                                0     2                         8
          vv
clus       WHITE
  subtype1    97
  subtype2    85
  subtype3    29
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   6        3        2
  BLACK OR AFRICAN AMERICAN              23       19        8
  WHITE                                  97       85       29
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 86 27
  subtype2 71 19
  subtype3 57 14
subtype1 subtype2 subtype3 
     113       90       71 
subtype1 subtype2 subtype3 
      27       19       14 
$subtype1
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-3810 
        5.06        37.02        43.43        17.79        35.11        36.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6782 
       22.52        24.13        25.18        20.61        24.69        20.28 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3697 
       62.96         6.97        61.02        78.08         6.05        85.05 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-A5EK 
        4.21         0.72         1.58         1.02         0.76         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4681 
        0.46        14.50        15.75         5.52        75.25        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 
       22.36        65.00        29.56         1.94         2.14         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
        0.26         1.35        48.20        21.99         2.01        37.02 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
        8.02        29.06        22.03         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       15.02        14.04        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       11.01        11.08        11.01        10.06        14.99        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6922 TCGA-DM-A0XF 
       11.51        18.25         1.32         4.50        10.13        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 
      130.65        49.91        13.32       140.38        44.32       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
        8.61        13.64        33.67         0.53        35.41        19.43 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       28.21        82.39        23.51        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       45.11        39.42        35.93        36.72        36.00        46.75 
TCGA-NH-A50T TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
        4.11        26.99        17.29         6.64        30.28 

$subtype2
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-A6-6653 TCGA-A6-6780 TCGA-A6-A566 
       30.44        33.53        22.06        24.39        20.12        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-5900 
        3.02        35.01        58.03         6.97        19.04         0.07 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AM-5821 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       21.37         0.79         0.92        21.44        17.82         5.19 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
        5.65        32.94        61.41        49.41         6.77        11.74 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        2.24         3.25        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-4747 
       51.32        21.14         2.93       124.27        20.02         8.02 
TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 
       27.02        16.01        15.02        14.04        13.05        11.08 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6538 
       12.03        12.26        19.59        17.75        15.12        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       16.14        12.39        12.43         9.44        13.41        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       10.26       119.70        24.43        92.75        12.59         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M 
      131.51       135.65         6.12        14.04        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6320 
       11.11         6.18        29.59       107.67        74.56        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
       10.98        10.52         2.79         5.98         5.59        14.76 

$subtype3
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-6141 
       13.94        37.05        37.25        31.63        22.09         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       25.08        24.16        21.76        23.87        19.66        16.24 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3510 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6965 
       61.84         1.02        63.98        56.55         0.10         0.20 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       27.09         0.20        50.37        58.39         1.41         5.13 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 
       62.79        12.10       100.01         5.23         3.19         3.06 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4748 
        3.29         0.33         0.10       102.44        23.05        26.04 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6164 
       13.02        22.98        30.08        15.02        12.00        29.03 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6534 
       14.99        12.99        12.95        20.19        20.42         7.92 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-6926 
       17.85        12.49        15.58         7.53        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A280 TCGA-F4-6460 TCGA-F4-6569 
       11.64         1.51        11.38         7.76        13.38        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 
       35.87         1.55        16.31        16.24         1.28         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6625 TCGA-G4-6627 
       43.07        53.62        51.75        91.79        47.15 

subtype1 subtype2 subtype3 
    0.07     0.07     0.10 
subtype1 subtype2 subtype3 
  140.38   135.65   102.44 
subtype1 subtype2 subtype3 
  22.030   17.345   15.580 
[1] "0.1 - 140.4 (22.0)" "0.1 - 135.7 (17.3)" "0.1 - 102.4 (15.6)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      16        0        6        32         1         1         3
  subtype2      19        1        3        29         3         0         4
  subtype3       6        0        5        28         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         20          8       10        10         0
  subtype2          2         12          8        4         4         1
  subtype3          3         11          7        6         2         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          16       19        6
  STAGE IA          0        1        0
  STAGE II          6        3        5
  STAGE IIA        32       29       28
  STAGE IIB         1        3        1
  STAGE IIC         1        0        0
  STAGE III         3        4        0
  STAGE IIIA        4        2        3
  STAGE IIIB       20       12       11
  STAGE IIIC        8        8        7
  STAGE IV         10        4        6
  STAGE IVA        10        4        2
  STAGE IVB         0        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 19 81 12
  subtype2  3 18 58 12
  subtype3  1  5 54 11
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        3        1
  T2       19       18        5
  T3       81       58       54
  T4       12       12       11
[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 63 32 19
  subtype2 58 19 15
  subtype3 42 19 10
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       63       58       42
  N1       32       19       19
  N2       19       15       10
[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 73 16   4   0 21
  subtype2 63  5   2   1 18
  subtype3 54  7   1   0  8
D4V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        73       63       54
  M1        16        5        7
  M1A        4        2        1
  M1B        0        1        0
  MX        21       18        8
[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"
D4V7, binary
          cls
clus        0  1
  subtype1 46 69
  subtype2 51 41
  subtype3 29 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   69
  subtype2   51   41
  subtype3   29   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       46       51       29
  MALE         69       41       42
[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"
D4V8, binary
          cls
clus         0   1
  subtype1 109   6
  subtype2  76  16
  subtype3  59  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109    6
  subtype2   76   16
  subtype3   59   12
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               109       76       59
  COLON MUCINOUS ADENOCARCINOMA        6       16       12
[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"
D4V9, binary
          cls
clus         0   1
  subtype1   2 113
  subtype2   0  92
  subtype3   1  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  113
  subtype2    0   92
  subtype3    1   70
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        1
  YES      113       92       70
[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 72  0  3  9
  subtype2 60  2  1 10
  subtype3 47  0  0  4
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       72       60       47
  R1        0        2        0
  R2        3        1        0
  RX        9       10        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"
D4V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        18
  subtype2                                0     2                        14
  subtype3                                1     5                        11
          vv
clus       WHITE
  subtype1    82
  subtype2    71
  subtype3    52
D4V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   4        2        5
  BLACK OR AFRICAN AMERICAN              18       14       11
  WHITE                                  82       71       52
[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 66 12
  subtype2 92 29
  subtype3 22  4
  subtype4 74 20
subtype1 subtype2 subtype3 subtype4 
      78      121       26       94 
subtype1 subtype2 subtype3 subtype4 
      12       29        4       20 
$subtype1
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       37.02        17.79        35.11        37.05        37.25        16.04 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       29.19        29.16         8.38        25.08        24.16        21.76 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3562 
       20.28         1.02        35.01         1.02        24.03        19.99 
TCGA-AA-3655 TCGA-AA-3678 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3837 
       61.02        47.01         0.99        35.05         0.99        38.99 
TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3971 
        0.99        53.00        17.03        33.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A02W TCGA-AD-5900 
       34.06        27.02        18.05        18.05        41.00         0.07 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-6607 TCGA-CA-5254 
        0.20        17.82        75.25        32.94         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
        3.06         3.29         0.33         1.35         2.01         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6167 
       29.06        22.03        22.98        30.08        17.03        14.99 
TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-6534 TCGA-D5-6922 TCGA-D5-6926 TCGA-DM-A1HA 
       11.08        12.26         7.92        10.13         9.04       131.51 
TCGA-DM-A280 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6704 
        7.76        26.47         8.61        13.64         6.18         1.55 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
        1.28         0.53        74.56        45.11        35.93        91.79 

$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-A6-6140 TCGA-A6-6650 
       22.06        32.71        27.09        22.52        24.13        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 
       24.69        23.87         3.02         1.02        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3548 
        6.97        38.99         9.07        19.07        34.03        33.99 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3664 TCGA-AA-3688 
       29.95        20.98        19.99        13.94        54.02        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3831 
        5.03        85.05        19.04         0.99        25.02        17.98 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3972 TCGA-AA-3973 
       14.93         0.99         2.01        20.98        50.99        13.05 
TCGA-AA-3989 TCGA-AA-A00E TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        7.96        30.02        42.02        17.03        14.99        34.98 
TCGA-AA-A01C TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       15.02        31.00        35.01         1.02        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 TCGA-AY-6197 
       39.98        40.96        56.55         1.58         0.20        21.44 
TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 
        5.65        22.36        65.00        61.41         6.77        29.56 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       11.74         1.94         2.14         3.25         0.07         0.26 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6165 
       21.99         2.93        37.02        15.02        15.02        16.04 
TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       21.99        11.01        13.05        11.08        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6920 
       13.51        11.51        18.25         4.50        17.13        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.43        14.30        12.00       119.70        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      140.38         7.50        44.32       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6806 TCGA-G4-6294 
       35.97        60.79        95.18        13.38        29.59        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 
        8.35        82.39        61.87        51.75        36.72        26.43 
TCGA-G4-6322 
       26.04 

$subtype3
TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3552 
       45.60        37.05         8.05        29.00        29.00        13.02 
TCGA-AA-3553 TCGA-AA-3854 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Z 
       24.00        36.03        13.94        34.03        17.03        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01P TCGA-AA-A01T TCGA-AA-A029 
       15.02         0.99        32.02        38.07        33.04        51.98 
TCGA-AA-A02K TCGA-AY-5543 TCGA-CM-5863 TCGA-CM-6164 TCGA-D5-6531 TCGA-D5-6898 
       14.01        15.75        15.02        29.03        17.75         7.53 
TCGA-F4-6855 TCGA-G4-6323 
       35.41        13.78 

$subtype4
TCGA-A6-3807 TCGA-A6-5661 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       34.65        33.53        25.18        24.39        20.12        19.66 
TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3833 
       17.95         0.92         5.98        26.99        33.04        15.95 
TCGA-AA-3841 TCGA-AA-3862 TCGA-AA-3869 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00A 
       36.95        30.05        27.02        24.00        19.07        38.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A02R TCGA-AA-A03F 
        4.01         0.99        31.00         1.02        22.03        18.05 
TCGA-AD-6548 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4323 
       21.37         0.46         0.92        27.09        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6718 
        5.13        49.41        12.10       100.01         5.23         0.10 
TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 
       21.14       124.27        23.05        20.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 
       13.02        16.01        15.02         5.03        12.00        14.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 
       12.99        13.02        15.02        14.04        12.95        11.01 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       19.59        20.19        20.42         1.32        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.49        16.14        15.58         9.44        11.64         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1HB 
       11.38        38.20       130.65        92.75        12.59       135.65 
TCGA-DM-A288 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 
       14.04        11.11        13.45        35.87        16.31        16.24 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
       33.67        19.43       107.67        23.51        43.07        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       44.68        55.04        39.42        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       26.17        46.75        47.15        52.80 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.99     0.10 
subtype1 subtype2 subtype3 subtype4 
  131.51   140.38    51.98   135.65 
subtype1 subtype2 subtype3 subtype4 
  21.020   20.980   22.995   19.625 
[1] "0.1 - 131.5 (21.0)" "0.1 - 140.4 (21.0)" "1.0 - 52.0 (23.0)" 
[4] "0.1 - 135.7 (19.6)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        0        6        23         3         0         2
  subtype2      18        0       10        34         3         1         8
  subtype3       3        1        1        12         0         0         2
  subtype4      18        0        3        39         2         0         6
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         14         10        5         4         0
  subtype2          2         18          8       18         5         1
  subtype3          0          3          3        1         1         0
  subtype4          3          8          8        4         4         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          10       18        3       18
  STAGE IA          0        0        1        0
  STAGE II          6       10        1        3
  STAGE IIA        23       34       12       39
  STAGE IIB         3        3        0        2
  STAGE IIC         0        1        0        0
  STAGE III         2        8        2        6
  STAGE IIIA        3        2        0        3
  STAGE IIIB       14       18        3        8
  STAGE IIIC       10        8        3        8
  STAGE IV          5       18        1        4
  STAGE IVA         4        5        1        4
  STAGE IVB         0        1        0        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0 12 59  9
  subtype2  2 21 90 15
  subtype3  0  3 22  1
  subtype4  4 17 62 13
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        0        2        0        4
  T2       12       21        3       17
  T3       59       90       22       62
  T4        9       15        1       13
[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 42 23 15
  subtype2 72 32 24
  subtype3 17  6  4
  subtype4 65 19 12
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       42       72       17       65
  N1       23       32        6       19
  N2       15       24        4       12
[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 65  6   3   0  5
  subtype2 92 23   0   1 11
  subtype3 24  2   0   0  1
  subtype4 78  5   3   0  9
D5V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        65       92       24       78
  M1         6       23        2        5
  M1A        3        0        0        3
  M1B        0        1        0        0
  MX         5       11        1        9
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 38 42
  subtype2 56 72
  subtype3 13 14
  subtype4 48 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   42
  subtype2   56   72
  subtype3   13   14
  subtype4   48   48
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       38       56       13       48
  MALE         42       72       14       48
[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"
D5V8, binary
          cls
clus         0   1
  subtype1  68  12
  subtype2 121   7
  subtype3  23   4
  subtype4  81  15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   12
  subtype2  121    7
  subtype3   23    4
  subtype4   81   15
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                68      121       23       81
  COLON MUCINOUS ADENOCARCINOMA       12        7        4       15
[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"
D5V9, binary
          cls
clus         0   1
  subtype1   2  78
  subtype2   1 127
  subtype3   0  27
  subtype4   0  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   78
  subtype2    1  127
  subtype3    0   27
  subtype4    0   96
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        1        0        0
  YES       78      127       27       96
[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 R2 RX
  subtype1 61  1  6
  subtype2 78 13  6
  subtype3 26  1  0
  subtype4 76  1  4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       61       78       26       76
  R2        1       13        1        1
  RX        6        6        0        4
[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"
D5V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         7
  subtype2                                0     5                         6
  subtype3                                0     0                         2
  subtype4                                0     1                         6
          vv
clus       WHITE
  subtype1    43
  subtype2    63
  subtype3     6
  subtype4    69
D5V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   5        5        0        1
  BLACK OR AFRICAN AMERICAN               7        6        2        6
  WHITE                                  43       63        6       69
[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 51  8
  subtype2 37  8
  subtype3 37 18
  subtype4 54 11
  subtype5 57 10
  subtype6 18 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      59       45       55       65       67       28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8        8       18       11       10       10 
$subtype1
TCGA-A6-2671 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5660 
       37.02        37.05        37.25        33.34        31.63        29.19 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6782 
       22.52        25.08        24.16        21.76        24.69        20.28 
TCGA-AA-3489 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3812 TCGA-AA-3866 TCGA-AA-A00J 
        1.02        20.98        19.99        35.05        17.03        18.05 
TCGA-AA-A00K TCGA-AA-A02W TCGA-AD-5900 TCGA-AM-5820 TCGA-AY-6196 TCGA-AZ-4308 
       18.05        41.00         0.07         0.46         0.20        75.25 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-5348 
        3.19         3.29         0.33         1.35         8.02        22.98 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        17.03        29.03        16.04        14.99 
TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       11.08        12.26         7.92        15.58         7.53        10.13 
TCGA-D5-6924 TCGA-D5-6926 TCGA-DM-A1D0 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A288 
       14.30         9.04       130.65        44.32       131.51        14.04 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        8.61        13.64        16.31         1.28         0.53        35.41 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
       74.56        43.07        45.11        35.93        91.79 

$subtype2
TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 
       46.65        17.79        42.28        35.11        15.52        16.04 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5667 
       32.75        36.53        32.91        30.44        23.61        29.16 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        3.02        35.01        58.03         1.02        38.99         9.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3655 
       19.07        34.03        33.99        24.00        19.99        61.02 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       54.02         0.92        47.01         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3955 
        0.99         0.99         0.99         0.99        53.00        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
       21.99        16.08        50.99        13.05        34.06        27.02 
TCGA-CK-6748 TCGA-CM-5341 TCGA-CM-6676 
        2.01        29.06        11.08 

$subtype3
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3831 TCGA-AA-3844 
       23.38        22.06        32.71         1.02        17.98        14.93 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-A01X TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4614 
        2.01        33.01        26.01        56.55         1.58         5.65 
TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 
       32.94        65.00        12.10        11.74         2.24         0.07 
TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5864 
        0.26        21.99        37.02        22.03        16.01        15.02 
TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5540 
       15.02        21.99        11.01        13.05        12.03        13.51 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6538 TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A0X9 
       11.51        18.25        17.13        12.43        12.00       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A28A TCGA-DM-A28C 
       92.75        49.91        13.32         7.50        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
      119.93        35.97        60.79        95.18        13.38        11.11 
TCGA-F4-6704 TCGA-F4-6806 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6303 
        1.55        29.59        28.21         8.35        23.51        61.87 
TCGA-G4-6315 
       36.72 

$subtype4
TCGA-A6-2681 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 
       45.60        22.09        27.09        24.13         8.38        20.61 
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3532 TCGA-AA-3555 TCGA-AA-3561 
       23.87        63.98         6.97        29.00        29.95        13.94 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3819 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3989 
        5.98        19.00        25.02         0.99        36.03         7.96 
TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U 
       13.94        30.02        34.03        17.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       32.02        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J 
       35.01        39.06        51.98         2.96        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6386 
        0.92        39.98        40.96         0.20        15.75        17.82 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CK-6747 
       22.36        61.41        29.56         1.94         3.25         2.93 
TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6920 TCGA-DM-A1D9 TCGA-DM-A282 
       10.06        15.12         4.50        12.39       140.38       139.17 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        26.43        26.04        13.78 

$subtype5
TCGA-A6-3807 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3554 
       34.65        25.18        24.39        20.12        19.66        17.95 
TCGA-AA-3710 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3862 TCGA-AA-3869 TCGA-AA-3950 
       26.99        15.95        36.95        30.05        27.02        24.00 
TCGA-AA-3986 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01K TCGA-AA-A01Q 
       19.07        38.04         4.01         0.99        31.00         1.02 
TCGA-AD-6548 TCGA-AM-5821 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       21.37         0.92        27.09        58.39         1.41         5.13 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
      100.01         5.23         0.10        21.14       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6168 
       20.02         8.02        13.02         5.03        14.04        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6529 
       13.02        14.04        12.95        11.01        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 
       20.42         1.32        12.49        16.14         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6569 TCGA-F4-6703 
        1.51        11.38        38.20       135.65        13.45        35.87 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 
       16.24        33.67        19.43        44.68        55.04        39.42 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       36.00        22.09        35.80        26.17        46.75        47.15 
TCGA-G4-6628 
       52.80 

$subtype6
TCGA-A6-5661 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3552 
       33.53        24.03        37.05         8.05        29.00        13.02 
TCGA-AA-3815 TCGA-AA-3837 TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02R TCGA-AA-A03F 
       33.04        38.99         2.01        14.01        22.03        18.05 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-4748 
       21.44        49.41         6.77         3.06         2.14        26.04 
TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6170 TCGA-D5-6531 TCGA-D5-6536 TCGA-DM-A1D8 
       30.08        12.00        15.02        17.75        17.85        12.59 
TCGA-DM-A280 TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6304 
        7.76         6.18       107.67        53.62 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.07     0.92     0.07     0.20     0.10     2.01 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  131.51    85.05   119.93   140.38   135.65   107.67 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   18.05    24.00    17.98    22.36    20.12    17.95 
[1] "0.1 - 131.5 (18.1)" "0.9 - 85.0 (24.0)"  "0.1 - 119.9 (18.0)"
[4] "0.2 - 140.4 (22.4)" "0.1 - 135.7 (20.1)" "2.0 - 107.7 (18.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       7        0        1        22         1         0         0
  subtype2      10        0        7         7         1         0         6
  subtype3       6        0        2        16         3         1         1
  subtype4       7        1        6        20         1         0         7
  subtype5      17        0        2        28         1         0         2
  subtype6       2        0        2        15         1         0         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         10          7        4         6         0
  subtype2          1          5          4        7         1         0
  subtype3          0         11          7        6         2         1
  subtype4          2         10          4        6         2         0
  subtype5          3          4          6        3         3         0
  subtype6          0          3          1        2         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           7       10        6        7       17        2
  STAGE IA          0        0        0        1        0        0
  STAGE II          1        7        2        6        2        2
  STAGE IIA        22        7       16       20       28       15
  STAGE IIB         1        1        3        1        1        1
  STAGE IIC         0        0        1        0        0        0
  STAGE III         0        6        1        7        2        2
  STAGE IIIA        2        1        0        2        3        0
  STAGE IIIB       10        5       11       10        4        3
  STAGE IIIC        7        4        7        4        6        1
  STAGE IV          4        7        6        6        3        2
  STAGE IVA         6        1        2        2        3        0
  STAGE IVB         0        0        1        0        0        0
[1] 13  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0  7 45  8
  subtype2  0 13 33  3
  subtype3  0  7 38 11
  subtype4  2  8 51  6
  subtype5  4 16 42  7
  subtype6  0  2 24  3
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        0        0        0        2        4        0
  T2        7       13        7        8       16        2
  T3       45       33       38       51       42       24
  T4        8        3       11        6        7        3
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 32 15 13
  subtype2 28 13  8
  subtype3 28 15 13
  subtype4 37 22  9
  subtype5 51 10  8
  subtype6 20  5  4
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       32       28       28       37       51       20
  N1       15       13       15       22       10        5
  N2       13        8       13        9        8        4
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B MX
  subtype1 46  7   3   0  3
  subtype2 40  8   0   0  1
  subtype3 42  8   0   1  5
  subtype4 51  8   0   0  9
  subtype5 57  3   3   0  6
  subtype6 23  2   0   0  2
D6V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0        46       40       42       51       57       23
  M1         7        8        8        8        3        2
  M1A        3        0        0        0        3        0
  M1B        0        0        1        0        0        0
  MX         3        1        5        9        6        2
[1] 5 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 27 33
  subtype2 25 24
  subtype3 23 33
  subtype4 34 34
  subtype5 29 40
  subtype6 17 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   33
  subtype2   25   24
  subtype3   23   33
  subtype4   34   34
  subtype5   29   40
  subtype6   17   12
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       27       25       23       34       29       17
  MALE         33       24       33       34       40       12
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 51  9
  subtype2 46  3
  subtype3 52  4
  subtype4 61  7
  subtype5 58 11
  subtype6 25  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    9
  subtype2   46    3
  subtype3   52    4
  subtype4   61    7
  subtype5   58   11
  subtype6   25    4
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                51       46       52       61       58
  COLON MUCINOUS ADENOCARCINOMA        9        3        4        7       11
                               clus
vv                              subtype6
  COLON ADENOCARCINOMA                25
  COLON MUCINOUS ADENOCARCINOMA        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1  2 58
  subtype2  0 49
  subtype3  1 55
  subtype4  0 68
  subtype5  0 69
  subtype6  0 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   58
  subtype2    0   49
  subtype3    1   55
  subtype4    0   68
  subtype5    0   69
  subtype6    0   29
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         2        0        1        0        0        0
  YES       58       49       55       68       69       29
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R2 RX
  subtype1 44  2  2
  subtype2 40  5  1
  subtype3 30  1  7
  subtype4 49  5  2
  subtype5 56  1  3
  subtype6 22  2  1
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       44       40       30       49       56       22
  R2        2        5        1        5        1        2
  RX        2        1        7        2        3        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         5
  subtype2                                0     0                         1
  subtype3                                1     4                         4
  subtype4                                0     1                         7
  subtype5                                0     1                         3
  subtype6                                0     2                         1
          vv
clus       WHITE
  subtype1    43
  subtype2    14
  subtype3    41
  subtype4    19
  subtype5    50
  subtype6    14
D6V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   3        0        4        1        1
  BLACK OR AFRICAN AMERICAN               5        1        4        7        3
  WHITE                                  43       14       41       19       50
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   2
  BLACK OR AFRICAN AMERICAN               1
  WHITE                                  14
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 105  31
  subtype2 118  30
  subtype3 110  27
subtype1 subtype2 subtype3 
     136      148      137 
subtype1 subtype2 subtype3 
      31       30       27 
$subtype1
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
        5.06        43.43        17.79        36.53        32.91        30.44 
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-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6782 
       25.08        25.18        20.61        21.76        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 
       61.84        52.44         9.63         1.02        37.05         1.02 
TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 
       62.96         6.97         1.02        19.07        29.00        26.01 
TCGA-AA-3660 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3973 
       78.08        37.05        85.05        17.03        24.03        13.05 
TCGA-AA-A00O TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F 
       27.02        15.02        15.02        26.01        37.02        39.98 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 
       14.01        41.00         4.21         0.79         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.43         0.46        14.50        15.75         5.19         5.52 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 
       22.36        62.79        29.56         1.94         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.07         0.26         1.35        48.20        21.99         2.01 
TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
        8.02        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 
       15.02        14.04        29.03        16.04        21.99        15.02 
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-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6922 
       18.25         1.32         4.50        17.13         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 
       12.43        14.30         9.04        13.41        11.38       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C 
       44.32       131.51       139.17         6.12        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97        60.79       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 
       13.38        13.64        33.67         1.28         0.53       107.67 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       28.21        23.51        61.87        44.68        55.04        45.11 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       35.93        36.72        36.00        46.75         4.11        10.98 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       26.99        17.29         6.64        30.28 

$subtype2
TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 
       43.76        13.94        37.05        37.25        16.04        33.34 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       14.53        31.63        33.53        22.09        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
        8.38        24.16        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3554 
       16.24        24.92         3.02        35.01        58.03        17.95 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3833 
       61.02         6.05         6.97        19.04         0.99        15.95 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A01P TCGA-AD-5900 
       29.98        31.00        26.01         2.01        38.07         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       21.37        56.55         0.72         1.58         1.02         0.76 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
        0.92        27.09         0.20        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 
       58.39         1.41         5.65        32.94         5.13        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       11.74         3.19         2.24         3.06         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       27.02        22.98        16.01        15.02        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       13.05        11.08        12.03        12.26        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.42        17.75         7.92        15.12        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        15.58        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB 
       12.00        10.26        24.43        49.91         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
        7.76        14.04        98.24        11.11        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6855 
       35.87         1.55        16.31        29.59        16.24        35.41 
TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       19.43         8.35        82.39        74.56        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       51.75        39.42        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        91.79        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
        2.79         5.98         5.59        14.76 

$subtype3
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-3494 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-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03         8.05        19.07        34.03        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99         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-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        30.05        53.00        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03        21.99        36.03        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
        0.99        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        33.04        35.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 
       18.05        40.96        16.31         0.95        75.25        83.80 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       37.02        26.04         8.02        13.02        29.06 

subtype1 subtype2 subtype3 
    0.07     0.07     0.92 
subtype1 subtype2 subtype3 
  140.38   135.65    83.80 
subtype1 subtype2 subtype3 
  20.445   16.935   24.000 
[1] "0.1 - 140.4 (20.4)" "0.1 - 135.7 (16.9)" "0.9 - 83.8 (24.0)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      22        0        8        38         1         1         4
  subtype2      24        1        7        54         2         0         5
  subtype3      26        0       12        41         6         0        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         21          9       13        13         0
  subtype2          4         20         15       12         3         1
  subtype3          4         14         14       17         1         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          22       24       26
  STAGE IA          0        1        0
  STAGE II          8        7       12
  STAGE IIA        38       54       41
  STAGE IIB         1        2        6
  STAGE IIC         1        0        0
  STAGE III         4        5       12
  STAGE IIIA        4        4        4
  STAGE IIIB       21       20       14
  STAGE IIIC        9       15       14
  STAGE IV         13       12       17
  STAGE IVA        13        3        1
  STAGE IVB         0        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   3  26  94  16
  subtype2   4  21 104  21
  subtype3   4  29 101  14
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        3        4        4
  T2       26       21       29
  T3       94      104      101
  T4       16       21       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 78 41 19
  subtype2 91 31 29
  subtype3 89 30 29
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       78       91       89
  N1       41       31       30
  N2       19       29       29
[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  90  19   7   0  22
  subtype2 108  14   0   1  25
  subtype3 127  17   1   0   0
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        90      108      127
  M1        19       14       17
  M1A        7        0        1
  M1B        0        1        0
  MX        22       25        0
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 61 78
  subtype2 73 78
  subtype3 72 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   78
  subtype2   73   78
  subtype3   72   76
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       61       73       72
  MALE         78       78       76
[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"
D7V8, binary
          cls
clus         0   1
  subtype1 134   5
  subtype2 119  32
  subtype3 126  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  134    5
  subtype2  119   32
  subtype3  126   20
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               134      119      126
  COLON MUCINOUS ADENOCARCINOMA        5       32       20
[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"
D7V9, binary
          cls
clus         0   1
  subtype1   2 137
  subtype2   1 150
  subtype3   0 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  137
  subtype2    1  150
  subtype3    0  148
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1        0
  YES      137      150      148
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  87   0   5  10
  subtype2  98   2   3  14
  subtype3 128   1  15   0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       87       98      128
  R1        0        2        1
  R2        5        3       15
  RX       10       14        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"
D7V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                        18
  subtype2                                1     6                        22
  subtype3                                0     0                         4
          vv
clus       WHITE
  subtype1    91
  subtype2   106
  subtype3    16
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   5        6        0
  BLACK OR AFRICAN AMERICAN              18       22        4
  WHITE                                  91      106       16
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  78  24
  subtype2  59  15
  subtype3  67  20
  subtype4 100  22
  subtype5  29   7
subtype1 subtype2 subtype3 subtype4 subtype5 
     102       74       87      122       36 
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       15       20       22        7 
$subtype1
TCGA-3L-AA1B TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5666 
        5.06        13.94        14.53        32.91        29.19        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6780 
       27.09        24.13        25.18        20.61        24.69        20.12 
TCGA-A6-A566 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3526 
       24.92        37.05         1.02        58.03        62.96        19.07 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-A01Z 
       61.02        78.08         6.05        37.05        85.05        37.02 
TCGA-AA-A02K TCGA-AA-A02Y TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 
       14.01        39.98        21.37         4.21         0.79         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L 
        0.20         0.43        14.50        15.75        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6608 TCGA-CA-5256 
        5.52        58.39        22.36        65.00         1.94         2.14 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        0.07         0.26        17.56       102.44        48.20        21.99 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 
        2.93       124.27         5.03        15.02        15.02        21.99 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        14.99        12.26 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19        18.25         1.32        15.12         4.50        17.13 
TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       15.58        13.41       119.70        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       140.38        44.32         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        6.12        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
      117.07        95.18        33.67       107.67        28.21         8.35 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       53.62        44.68        55.04        36.72        36.00        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX TCGA-RU-A8FL 
        4.11        10.98        10.52        26.99        17.29        30.28 

$subtype2
TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       43.43        37.05        37.25        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 
       22.09        29.16        22.52        25.08        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3511 
       20.28        61.84        52.44         9.63         1.02         6.97 
TCGA-AA-A01X TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 TCGA-AZ-4323 TCGA-AZ-5403 
       26.01         1.58         1.02         0.46         1.41        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6748 
       29.56         5.23         3.29         0.33         1.35         2.01 
TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5868 
        8.02        22.03        22.98        30.08        16.01        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6534 
       15.02        10.06        13.51        11.51        17.75         7.92 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 
        7.53        10.13        12.43        14.30         9.04        11.38 
TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 
       26.47         8.61        13.38        13.64         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-G4-6311 TCGA-G4-6314 TCGA-G4-6625 
       43.07        61.87        45.11        39.42        35.93        91.79 
TCGA-G4-6627 TCGA-QG-A5Z1 
       47.15         6.64 

$subtype3
TCGA-A6-2686 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 
       16.04        33.53        22.06         8.38        24.16        24.39 
TCGA-A6-6781 TCGA-A6-A565 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3663 TCGA-AA-3713 
       19.66        16.24         3.02        35.01         6.97        19.04 
TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 
       38.07         0.07        56.55         0.72         0.76         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4313 TCGA-AZ-4614 TCGA-AZ-4615 
       27.09         0.20        21.44        50.37         5.65        32.94 
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-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6718 
       11.74         3.19         2.24         3.06         3.25         0.10 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
       40.34        70.16        15.62        51.32        21.14        23.05 
TCGA-CM-4744 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6171 
       20.02        27.02        15.02        15.02        12.00        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6536 
       12.95        13.05        12.03        19.59        20.42        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.49        16.14        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA 
       12.00        10.26        24.43        49.91         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      135.65        98.24        11.11        13.45         6.18        35.87 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 
       29.59        19.43        74.56        51.75        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       26.04        13.78        35.80        26.17        52.80         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
        5.98         5.59        14.76 

$subtype4
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-A6-4107 TCGA-AA-3488 TCGA-AA-3494 
       15.52        34.65        36.53        32.45         5.03         1.02 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       19.99        13.94        19.99         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 
       50.04        47.01        15.02        11.01        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
        5.03        35.05         0.99        25.02        17.98        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3862 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3970 
       24.00         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-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        17.03        27.02        42.02        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-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       35.01        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        5.03         0.92        41.00        18.05        40.96        16.31 
TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
        0.95        75.25        83.80        37.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5341 
       13.02        29.06 

$subtype5
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3809 TCGA-AA-3516 
       46.65        43.76        23.38        33.34        32.75        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3664 
        1.02         8.05         0.99        17.95        29.95        54.02 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3821 
        5.98        26.99         0.99         0.99        33.04         1.02 
TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       15.95        53.00        31.00         2.01        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-A01Q TCGA-AA-A01R TCGA-AA-A02R 
       18.05         4.01         0.99         1.02        35.01        22.03 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.33     0.07     0.92     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
  140.38    91.79   135.65    83.80    54.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   20.40    16.14    16.14    24.00    23.69 
[1] "0.1 - 140.4 (20.4)" "0.3 - 91.8 (16.1)"  "0.1 - 135.7 (16.1)"
[4] "0.9 - 83.8 (24.0)"  "1.0 - 54.0 (23.7)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      17        0        7        31         1         1         3
  subtype2       7        0        3        24         1         0         2
  subtype3      18        1        4        30         1         0         4
  subtype4      26        0        8        34         2         0         8
  subtype5       4        0        5        14         4         0         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2         16          6        7         9         0
  subtype2          2         15          6        6         6         0
  subtype3          3          9         10        5         1         1
  subtype4          5         10         16       22         1         0
  subtype5          0          5          0        2         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          17        7       18       26        4
  STAGE IA          0        0        1        0        0
  STAGE II          7        3        4        8        5
  STAGE IIA        31       24       30       34       14
  STAGE IIB         1        1        1        2        4
  STAGE IIC         1        0        0        0        0
  STAGE III         3        2        4        8        4
  STAGE IIIA        2        2        3        5        0
  STAGE IIIB       16       15        9       10        5
  STAGE IIIC        6        6       10       16        0
  STAGE IV          7        6        5       22        2
  STAGE IVA         9        6        1        1        0
  STAGE IVB         0        0        1        0        0
[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       T1 T2 T3 T4
  subtype1  2 19 71 12
  subtype2  1  8 54 11
  subtype3  3 16 58 11
  subtype4  4 29 88 11
  subtype5  1  4 28  6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        1        3        4        1
  T2       19        8       16       29        4
  T3       71       54       58       88       28
  T4       12       11       11       11        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 65 24 14
  subtype2 36 26 12
  subtype3 56 17 16
  subtype4 73 29 30
  subtype5 28  6  5
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       65       36       56       73       28
  N1       24       26       17       29        6
  N2       14       12       16       30        5
[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  70  11   4   0  18
  subtype2  49   9   3   0  13
  subtype3  63   6   0   1  16
  subtype4 107  22   1   0   0
  subtype5  36   2   0   0   0
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        70       49       63      107       36
  M1        11        9        6       22        2
  M1A        4        3        0        1        0
  M1B        0        0        1        0        0
  MX        18       13       16        0        0
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 47 57
  subtype2 31 43
  subtype3 40 49
  subtype4 64 68
  subtype5 24 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   57
  subtype2   31   43
  subtype3   40   49
  subtype4   64   68
  subtype5   24   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       47       31       40       64       24
  MALE         57       43       49       68       15
[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"
D8V8, binary
          cls
clus         0   1
  subtype1  96   8
  subtype2  67   7
  subtype3  71  18
  subtype4 122   8
  subtype5  23  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96    8
  subtype2   67    7
  subtype3   71   18
  subtype4  122    8
  subtype5   23   16
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                96       67       71      122       23
  COLON MUCINOUS ADENOCARCINOMA        8        7       18        8       16
[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"
D8V9, binary
          cls
clus         0   1
  subtype1   1 103
  subtype2   2  72
  subtype3   0  89
  subtype4   0 132
  subtype5   0  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  103
  subtype2    2   72
  subtype3    0   89
  subtype4    0  132
  subtype5    0   39
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        2        0        0        0
  YES      103       72       89      132       39
[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  58   0   2  10
  subtype2  54   0   0   5
  subtype3  56   2   1   9
  subtype4 110   1  19   0
  subtype5  35   0   1   0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       58       54       56      110       35
  R1        0        0        2        1        0
  R2        2        0        1       19        1
  RX       10        5        9        0        0
[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"
D8V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        16
  subtype2                                1     3                        11
  subtype3                                0     5                        13
  subtype4                                0     0                         4
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    71
  subtype2    56
  subtype3    66
  subtype4    15
  subtype5     5
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   3        3        5        0        0
  BLACK OR AFRICAN AMERICAN              16       11       13        4        0
  WHITE                                  71       56       66       15        5
[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"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 127  31
  subtype2  52  14
  subtype3 129  36
subtype1 subtype2 subtype3 
     158       66      165 
subtype1 subtype2 subtype3 
      31       14       36 
$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-A6-6140 TCGA-A6-6142 
       22.06        32.71        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3496 
       25.18        20.61        24.39        20.12        20.28         1.02 
TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 
        6.97        61.02        78.08         6.05         6.97        85.05 
TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       19.04         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
        0.10         0.20         0.92        14.50        27.09        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 
        0.20        21.44        17.82         5.13        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        6.77        12.10        11.74         1.94         2.24         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        15.62        48.20        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 
        2.93       124.27        23.05        27.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A0X9 
       15.58        12.39        12.43        13.41        12.00       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6463 
       35.97        60.79       117.07        98.24        95.18        13.64 
TCGA-F4-6570 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        6.18        33.67        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        51.75        39.42        36.72        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 
       46.75        52.80 

$subtype2
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5662 
       45.60        37.05        37.25        33.34        31.63        23.61 
TCGA-A6-5664 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.09        22.52         8.38        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X 
       23.87        19.66         1.02        27.02        38.07        26.01 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AZ-4323 
        0.72         1.58         1.02         0.76         0.46         1.41 
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 
       62.79       100.01        29.56         5.23         3.19         3.06 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-4748 TCGA-CM-6162 TCGA-CM-6167 
        0.33         0.10         2.01        26.04        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6898 
       12.99        12.95        10.06        19.59         7.92         7.53 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
       11.38        10.26         8.61        13.38        11.11        13.45 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        16.24         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6627 
        0.53        19.43        43.07        45.11        35.93        47.15 

$subtype3
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       37.02        46.65        43.76        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        13.94        15.52        16.04        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3494 
       32.75        36.53        32.45         5.03         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3514 
       37.05        35.01        58.03        62.96        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 
       20.98        19.99        13.94        19.99        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99         0.99         0.99        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-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-3994 TCGA-AA-A00D 
       27.02        27.02        19.07         7.96        27.02        19.00 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       18.05        17.03        42.02        17.03        14.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 
       18.05        40.96        16.31         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-CA-5256 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
        2.14        70.16        20.02        37.02         8.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-DM-A1D6 
       13.02        29.06        49.91 

subtype1 subtype2 subtype3 
    0.07     0.10     0.92 
subtype1 subtype2 subtype3 
  140.38   100.01    83.80 
subtype1 subtype2 subtype3 
  20.350   13.415   24.000 
[1] "0.1 - 140.4 (20.4)" "0.1 - 100.0 (13.4)" "0.9 - 83.8 (24.0)" 
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      24        1        7        56         2         1         7
  subtype2       7        0        3        21         0         0         2
  subtype3      35        0       18        44         6         0        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         24         11       11         7         1
  subtype2          3         10          8        4         4         0
  subtype3          4         15         13       27         5         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          24        7       35
  STAGE IA          1        0        0
  STAGE II          7        3       18
  STAGE IIA        56       21       44
  STAGE IIB         2        0        6
  STAGE IIC         1        0        0
  STAGE III         7        2       12
  STAGE IIIA        4        3        4
  STAGE IIIB       24       10       15
  STAGE IIIC       11        8       13
  STAGE IV         11        4       27
  STAGE IVA         7        4        5
  STAGE IVB         1        0        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   5  24 115  15
  subtype2   0   9  46  11
  subtype3   6  36 118  20
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        0        6
  T2       24        9       36
  T3      115       46      118
  T4       15       11       20
[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  98  39  22
  subtype2  33  19  14
  subtype3 108  37  35
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       98       33      108
  N1       39       19       37
  N2       22       14       35
[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 113  12   5   1  26
  subtype2  48   8   0   0   9
  subtype3 144  30   2   0   1
D9V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       113       48      144
  M1        12        8       30
  M1A        5        0        2
  M1B        1        0        0
  MX        26        9        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"
D9V7, binary
          cls
clus        0  1
  subtype1 74 86
  subtype2 27 39
  subtype3 90 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74   86
  subtype2   27   39
  subtype3   90   90
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       74       27       90
  MALE         86       39       90
[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"
D9V8, binary
          cls
clus         0   1
  subtype1 145  15
  subtype2  53  13
  subtype3 153  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  145   15
  subtype2   53   13
  subtype3  153   25
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               145       53      153
  COLON MUCINOUS ADENOCARCINOMA       15       13       25
[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"
D9V9, binary
          cls
clus         0   1
  subtype1   0 160
  subtype2   2  64
  subtype3   1 179
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  160
  subtype2    2   64
  subtype3    1  179
     clus
vv    subtype1 subtype2 subtype3
  NO         0        2        1
  YES      160       64      179
[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  94   1   2  15
  subtype2  43   0   0   5
  subtype3 145   2  23   2
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       94       43      145
  R1        1        0        2
  R2        2        0       23
  RX       15        5        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"
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        12
  subtype2                                1     3                         7
  subtype3                                0     1                         4
          vv
clus       WHITE
  subtype1   132
  subtype2    51
  subtype3    30
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   7        3        1
  BLACK OR AFRICAN AMERICAN              12        7        4
  WHITE                                 132       51       30
[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 103  30
  subtype2  41   9
  subtype3  59  15
  subtype4 105  27
subtype1 subtype2 subtype3 subtype4 
     133       50       74      132 
subtype1 subtype2 subtype3 subtype4 
      30        9       15       27 
$subtype1
TCGA-A6-2675 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5665 
       43.43        14.53        32.91        30.44        33.53        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       32.71        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3660 
        1.02        35.01         6.97         1.02        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A01Z 
        6.05         6.97        85.05        19.04        34.98        37.02 
TCGA-AA-A02H TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        2.01         4.21        56.55         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.10        14.50        15.75         0.20        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 
        1.41         5.13        61.41        49.41        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4947 
       11.74         1.94         2.24         3.06         3.25        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 
       40.34        15.62        48.20        51.32         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       23.05        27.02        22.98        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       15.02        14.04        29.03        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.03        14.99        11.51        20.19        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       15.12         4.50        12.49        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.43        11.64       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76        14.04        26.47        81.37       119.93 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6570 TCGA-F4-6806 
      117.07        98.24        95.18        11.11         6.18        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.24        33.67        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       82.39        53.62        44.68        51.75        39.42        36.00 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        26.04        35.80        26.17        91.79        46.75 
TCGA-G4-6628 
       52.80 

$subtype2
TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6654 TCGA-AD-5900 
       31.63        23.61        29.16        24.16        23.87         0.07 
TCGA-AD-6895 TCGA-AM-5820 TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-AZ-6603 
        0.72         0.46        27.09        62.79       100.01        29.56 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 
        3.19         0.33         0.10         1.35        21.14         2.01 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       22.03        30.08        15.02        17.03        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6534 
       14.99        12.99        12.95        19.59        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       17.85         7.53        10.13         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       11.38        10.26         8.61        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 
       16.31         1.28         0.53        43.07        61.87        45.11 
TCGA-G4-6320 TCGA-G4-6627 
       26.43        47.15 

$subtype3
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6142 
       43.76        17.79        42.28        29.19        22.09        25.08 
TCGA-A6-6651 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3517 
       21.76         1.02         1.02        58.03        62.96        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        9.07        24.03        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3678 TCGA-AA-3680 
       12.99        23.01        13.94        19.99        47.01        11.01 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3867 
       36.00         5.03        25.02        17.98        38.99        24.03 
TCGA-AA-3875 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00U 
       18.05        26.01        19.07         7.96        17.03        17.03 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02J TCGA-AA-A02K TCGA-AD-6548 TCGA-AD-6964 
        1.02        26.01         5.03        14.01        21.37         0.76 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-6599 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        0.20        16.31         6.77         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-6161 
        0.26       102.44        21.99         8.02        13.02        15.02 
TCGA-CM-6166 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6924 
       21.99        12.26        13.51         1.32        17.13        14.30 
TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G 
       13.41        38.20       139.17         6.12        35.97        60.79 
TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6307 TCGA-G4-6314 
       13.38        13.64         8.35        23.51        55.04        35.93 
TCGA-G4-6315 TCGA-G4-6323 
       36.72        13.78 

$subtype4
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-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 
       33.34        32.75        36.53        32.45         5.03         3.02 
TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 
       37.05        63.98         1.02        13.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
        8.05        19.07        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       19.99        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3710 
       47.05        15.02         5.98        37.05        19.00        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
        0.99         0.99        35.05        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-A00D TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q 
       27.02        27.02        19.00        18.05        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01R 
       14.99         0.99        32.02        12.00        38.07        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        35.01        39.06        51.98         2.96        39.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AM-5821 
        0.92        22.03        39.98        18.05        40.96         0.92 
TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        0.95        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CK-4951 TCGA-CM-4744 TCGA-CM-4746 
       83.80        22.36        65.00        70.16        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-D5-6931 TCGA-DM-A1HA TCGA-G4-6299 
        8.02        26.04        29.06        12.00       131.51        74.56 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.07     0.92 
subtype1 subtype2 subtype3 subtype4 
  140.38   100.01   139.17   131.51 
subtype1 subtype2 subtype3 subtype4 
  20.120   15.005   18.015   27.020 
[1] "0.1 - 140.4 (20.1)" "0.1 - 100.0 (15.0)" "0.1 - 139.2 (18.0)"
[4] "0.9 - 131.5 (27.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      20        0        7        50         4         1         6
  subtype2       6        0        2        19         0         0         1
  subtype3      11        1        4        19         0         0         4
  subtype4      29        0       15        33         4         0        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3         15         10        9         6         1
  subtype2          3          8          2        3         4         0
  subtype3          3         12          8       14         1         0
  subtype4          2         14         12       16         5         0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          20        6       11       29
  STAGE IA          0        0        1        0
  STAGE II          7        2        4       15
  STAGE IIA        50       19       19       33
  STAGE IIB         4        0        0        4
  STAGE IIC         1        0        0        0
  STAGE III         6        1        4       10
  STAGE IIIA        3        3        3        2
  STAGE IIIB       15        8       12       14
  STAGE IIIC       10        2        8       12
  STAGE IV          9        3       14       16
  STAGE IVA         6        4        1        5
  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       T1 T2 T3 T4
  subtype1  4 21 94 17
  subtype2  1  6 39  4
  subtype3  2 13 56  7
  subtype4  4 29 90 18
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        1        2        4
  T2       21        6       13       29
  T3       94       39       56       90
  T4       17        4        7       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"
          vv
clus       N0 N1 N2
  subtype1 90 26 19
  subtype2 27 17  6
  subtype3 38 21 20
  subtype4 84 31 26
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       90       27       38       84
  N1       26       17       21       31
  N2       19        6       20       26
[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  97  11   3   1  21
  subtype2  36   6   1   0   7
  subtype3  55  14   1   0   8
  subtype4 117  19   2   0   0
D10V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        97       36       55      117
  M1        11        6       14       19
  M1A        3        1        1        2
  M1B        1        0        0        0
  MX        21        7        8        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"
D10V7, binary
          cls
clus        0  1
  subtype1 57 79
  subtype2 23 27
  subtype3 40 39
  subtype4 71 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   79
  subtype2   23   27
  subtype3   40   39
  subtype4   71   70
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       57       23       40       71
  MALE         79       27       39       70
[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"
D10V8, binary
          cls
clus         0   1
  subtype1 120  16
  subtype2  40  10
  subtype3  71   7
  subtype4 120  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  120   16
  subtype2   40   10
  subtype3   71    7
  subtype4  120   20
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA               120       40       71      120
  COLON MUCINOUS ADENOCARCINOMA       16       10        7       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus         0   1
  subtype1   0 136
  subtype2   2  48
  subtype3   0  79
  subtype4   1 140
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  136
  subtype2    2   48
  subtype3    0   79
  subtype4    1  140
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        2        0        1
  YES      136       48       79      140
[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  76   1   3  11
  subtype2  37   0   0   5
  subtype3  51   1   9   5
  subtype4 118   1  13   1
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       76       37       51      118
  R1        1        0        1        1
  R2        3        0        9       13
  RX       11        5        5        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"
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        11
  subtype2                                1     3                         3
  subtype3                                0     4                         6
  subtype4                                0     0                         3
          vv
clus       WHITE
  subtype1   106
  subtype2    43
  subtype3    32
  subtype4    32
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   4        3        4        0
  BLACK OR AFRICAN AMERICAN              11        3        6        3
  WHITE                                 106       43       32       32
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 17 12
  subtype2 22 10
  subtype3 19  5
subtype1 subtype2 subtype3 
      29       32       24 
subtype1 subtype2 subtype3 
      12       10        5 
$subtype1
TCGA-A6-2675 TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3511 TCGA-AD-6901 TCGA-AD-6963 
       43.43         8.38        20.28         6.97         1.02         0.10 
TCGA-AD-6964 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CM-6674 TCGA-CM-6676 
        0.76         5.13        29.56         5.23        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-DM-A0XD 
       11.08        11.01        10.06        12.03        14.99        24.43 
TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A280 TCGA-DM-A282 
       38.20        13.32        12.59       140.38         7.76       139.17 
TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6625 
        6.12         6.18        33.67        74.56        91.79 

$subtype2
TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 
       31.63        29.16        25.08        24.16        21.76        23.87 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-5403 
       19.66         1.02         0.07         0.20         1.41        62.79 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 
       12.10       100.01         3.19         0.10         1.35        21.14 
TCGA-CK-6748 TCGA-CM-5860 TCGA-CM-6167 TCGA-D5-6534 TCGA-F4-6459 TCGA-F4-6460 
        2.01        16.01        14.99         7.92         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6302 
       13.45         1.55        16.31        16.24         1.28        43.07 
TCGA-G4-6314 TCGA-G4-6627 
       35.93        47.15 

$subtype3
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6548 
       27.09        22.52        24.13        20.61        24.39        21.37 
TCGA-AD-6889 TCGA-AD-6965 TCGA-AZ-6598 TCGA-CM-4751 TCGA-D5-6533 TCGA-D5-6536 
       56.55         0.20        49.41        27.02         1.32        17.85 
TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F 
       10.13        14.30       130.65         7.50       131.51        35.97 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6628 
       28.21         8.35        61.87        44.68        51.75        52.80 

subtype1 subtype2 subtype3 
    0.10     0.07     0.20 
subtype1 subtype2 subtype3 
  140.38   100.01   131.51 
subtype1 subtype2 subtype3 
  12.030   15.500   25.705 
[1] "0.1 - 140.4 (12.0)" "0.1 - 100.0 (15.5)" "0.2 - 131.5 (25.7)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2        1        13         1          0          2
  subtype2       3        3         7         0          0          7
  subtype3       4        2         7         0          1          5
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          2        2         1
  subtype2          5        5         2
  subtype3          2        2         0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        3        4
  STAGE II          1        3        2
  STAGE IIA        13        7        7
  STAGE IIB         1        0        0
  STAGE IIIA        0        0        1
  STAGE IIIB        2        7        5
  STAGE IIIC        2        5        2
  STAGE IV          2        5        2
  STAGE IVA         1        2        0
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1  2 21  5
  subtype2  1  2 25  4
  subtype3  0  5 17  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        1        1        0
  T2        2        2        5
  T3       21       25       17
  T4        5        4        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"
          vv
clus       N0 N1 N2
  subtype1 19  4  6
  subtype2 13 11  8
  subtype3 14  7  3
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       19       13       14
  N1        4       11        7
  N2        6        8        3
[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 MX
  subtype1 18  2   1  6
  subtype2 18  6   1  6
  subtype3 20  2   0  2
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        18       18       20
  M1         2        6        2
  M1A        1        1        0
  MX         6        6        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"
D11V7, binary
          cls
clus        0  1
  subtype1 14 15
  subtype2 15 17
  subtype3  9 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   15
  subtype2   15   17
  subtype3    9   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       15        9
  MALE         15       17       15
[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"
D11V8, binary
          cls
clus        0  1
  subtype1 26  3
  subtype2 25  7
  subtype3 24  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    3
  subtype2   25    7
  subtype3   24    0
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                26       25       24
  COLON MUCINOUS ADENOCARCINOMA        3        7        0
[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"
D11V9, binary
          cls
clus        0
  subtype1 29
  subtype2 32
  subtype3 24
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 RX
  subtype1 12  1
  subtype2 19  4
  subtype3 11  0
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       12       19       11
  RX        1        4        0
[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"
D11V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                1     2                         3
  subtype3                                0     1                         2
          vv
clus       WHITE
  subtype1    27
  subtype2    25
  subtype3    21
D11V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        2        1
  BLACK OR AFRICAN AMERICAN               1        3        2
  WHITE                                  27       25       21
[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  8  4
  subtype2 15  7
  subtype3 12  5
  subtype4 17  7
  subtype5  6  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      12       22       17       24       10 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        7        5        7        4 
$subtype1
TCGA-A6-2675 TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-6901 TCGA-AY-6196 TCGA-AZ-5403 
       43.43        20.28         1.02         1.02         0.20        62.79 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-CM-5860 TCGA-CM-6677 TCGA-CM-6679 TCGA-F4-6569 
       12.10         5.23        16.01        11.08        10.06        13.45 

$subtype2
TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-AD-6548 
       31.63        29.16        25.08        21.76        23.87        21.37 
TCGA-AZ-4323 TCGA-AZ-6603 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-6167 TCGA-D5-6922 
        1.41        29.56         1.35         2.01        14.99        10.13 
TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        6.12         8.61        13.38        16.31        16.24         1.28 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6627 
       43.07        61.87        35.93        47.15 

$subtype3
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6965 
       27.09        24.13        20.61        24.39        56.55         0.20 
TCGA-AZ-6598 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F 
       49.41        24.43       130.65         7.50       131.51        35.97 
TCGA-F4-6808 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6306 TCGA-G4-6309 
       33.67        28.21         8.35        44.68        51.75 

$subtype4
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6781 TCGA-AD-5900 TCGA-AD-6963 
       22.52         8.38        24.16        19.66         0.07         0.10 
TCGA-AD-6964 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-6718 TCGA-CK-5916 
        0.76         5.13       100.01         3.19         0.10        21.14 
TCGA-CM-4751 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6534 TCGA-D5-6536 
       27.02        12.95        11.01        12.03         7.92        17.85 
TCGA-DM-A280 TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6625 TCGA-G4-6628 
        7.76         6.18         1.55        74.56        91.79        52.80 

$subtype5
TCGA-AA-3511 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A0XF 
        6.97        11.08        14.99         1.32        14.30        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A282 
       13.32        12.59       140.38       139.17 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     1.28     0.20     0.07     1.32 
subtype1 subtype2 subtype3 subtype4 subtype5 
   62.79    61.87   131.51   100.01   140.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
   11.59    18.84    28.21    11.52    13.81 
[1] "0.2 - 62.8 (11.6)"  "1.3 - 61.9 (18.8)"  "0.2 - 131.5 (28.2)"
[4] "0.1 - 100.0 (11.5)" "1.3 - 140.4 (13.8)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        2         4         1          0          1
  subtype2       1        0         4         0          1          6
  subtype3       2        2         6         0          0          3
  subtype4       4        1         8         0          0          3
  subtype5       1        1         5         0          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        1         0
  subtype2          2        5         2
  subtype3          2        1         0
  subtype4          3        2         1
  subtype5          1        0         0
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        2        4        1
  STAGE II          2        0        2        1        1
  STAGE IIA         4        4        6        8        5
  STAGE IIB         1        0        0        0        0
  STAGE IIIA        0        1        0        0        0
  STAGE IIIB        1        6        3        3        1
  STAGE IIIC        1        2        2        3        1
  STAGE IV          1        5        1        2        0
  STAGE IVA         0        2        0        1        0
[1] 9 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       T1 T2 T3 T4
  subtype1  0  1  8  3
  subtype2  0  2 19  1
  subtype3  1  2 13  1
  subtype4  1  3 16  4
  subtype5  0  1  7  2
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        0        0        1        1        0
  T2        1        2        2        3        1
  T3        8       19       13       16        7
  T4        3        1        1        4        2
[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  9  2  1
  subtype2  5 11  6
  subtype3 10  4  3
  subtype4 14  4  6
  subtype5  8  1  1
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        9        5       10       14        8
  N1        2       11        4        4        1
  N2        1        6        3        6        1
[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 MX
  subtype1  6  1   0  4
  subtype2 12  6   1  3
  subtype3 14  1   0  2
  subtype4 16  2   1  4
  subtype5  8  0   0  1
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0         6       12       14       16        8
  M1         1        6        1        2        0
  M1A        0        1        0        1        0
  MX         4        3        2        4        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"
D12V7, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2 17  5
  subtype3  7 10
  subtype4  8 16
  subtype5  5  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2   17    5
  subtype3    7   10
  subtype4    8   16
  subtype5    5    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        1       17        7        8        5
  MALE         11        5       10       16        5
[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"
D12V8, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2 19  3
  subtype3 17  0
  subtype4 19  5
  subtype5  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   19    3
  subtype3   17    0
  subtype4   19    5
  subtype5    9    1
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                11       19       17       19        9
  COLON MUCINOUS ADENOCARCINOMA        1        3        0        5        1
[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"
D12V9, binary
          cls
clus        0
  subtype1 12
  subtype2 22
  subtype3 17
  subtype4 24
  subtype5 10
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 RX
  subtype1  7  0
  subtype2 14  2
  subtype3  4  0
  subtype4 13  2
  subtype5  4  1
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0        7       14        4       13        4
  RX        0        2        0        2        1
[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"
D12V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         1
  subtype2                                0     1                         2
  subtype3                                0     1                         2
  subtype4                                1     1                         1
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    10
  subtype2    19
  subtype3    14
  subtype4    21
  subtype5     9
D12V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   0        1        1        1        0
  BLACK OR AFRICAN AMERICAN               1        2        2        1        0
  WHITE                                  10       19       14       21        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"
