[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/10005863/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/10668133/COAD-TP.mergedcluster.txt"

nPatients in clinical file=441, in cluster file=447, common to both=439
[1]  12 439
[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   4 
 36 151 191  52 
  1   2   3   4 
 36 151 191  52 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
113  91  71 
  1   2   3 
113  91  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   4   5 
 35 114  72  90 119 
  1   2   3   4   5 
 35 114  72  90 119 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 74  97  88 132  39 
  1   2   3   4   5 
 74  97  88 132  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 
79 78 63 
 1  2  3 
79 78 63 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
66 51 83 20 
 1  2  3  4 
66 51 83 20 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 439 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
         154         1126         1419         1331         1321          711 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
         541         1286         1366         1068         1387           NA 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3808 
         472         1127         1133          488         1054         1014 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
         996         1111           NA          987         1001          962 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
         926          888         1020          718          672          671 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
         995          887          824          685          734          255 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
         763          766          735          627          662          751 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
         742          726          612          598          617           NA 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
          NA           NA         1595          293           NA           31 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
          NA           31         1127           31         1065         1765 
TCGA-AA-3509 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1915         1946          212           31           NA         1186 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 
          31          276          731           NA         1127         1096 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
         245          580           NA           NA          580         1035 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
         882          882          791          395           30          426 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        1034          639           NA          730          546          911 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
         700          638          608          424          608         1856 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
        2375          184          212         1643           NA          426 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
          28         1522         1431         1430          457           NA 
TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 
         182           NA         1127          578           NA           NA 
TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 
          NA           NA         2587          821           NA          579 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3815 TCGA-AA-3818 
          30           30         1066           NA         1005           NA 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
         761           31          547          485         1186         1124 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
        1126          454           NA          518           30           NA 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        1006           NA         1096          975           30          945 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
         945           NA          914         1612          518          731 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA          912           NA          549          943           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
         395          730         1004          791          730           NA 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 
         638         1035           61          669         1096          489 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        1551          397         1036          791          761          730 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
         822          822           NA          580           NA          822 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
         424         1157          578          913         1035          549 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
         549          518           NA          822         1278           30 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
         518          456          669         1064          457          457 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
          30          974          365          943          943           NA 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
          31         1065           31         1005         1065          791 
TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1126           NA           NA         1581           NA         1216 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
          NA           NA           NA           28           NA         1247 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        1216           NA         1246            2          650          128 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        1720           24           22           48           31            3 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
          23            6           NA           13           14           28 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
         441          824           NA           NA          479            6 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
         652          542          158          168         2289         1532 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
        1776           NA           NA         1002           NA         2549 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
          NA         1977           NA         1868           NA           NA 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
          NA           68           93           65           99          100 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
           2            8           10            3           41          534 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        3116         1227         2134          475         1466         1561 
TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 
         669           NA           NA           NA           89           61 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
        3780          701          609         1126          244          792 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
         244          822          396          884          670          699 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
         915          487          457           NA          457          457 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
         518          457          365          427          883          488 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
         669          456          395          396          457          427 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
         335          394          397          337          337          335 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
         306          366          456          373          596          411 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
         350          614          621          540          555           40 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
         241          460          543          137          521          380 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
         491          474          229          377          308          378 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
         435          275          287          354          408           46 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
         365          346          312         3641          743         1162 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
        3974         2821         1518          405          383         4270 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
         228         1348         4000         4126          236         4233 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
         186          427          805         2475         3648         1094 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
        1849         3561         2988         2895           NA          407 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
          NA          415          409           NA         1091           47 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
         496          900          494         1024           39           16 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        1077          591         3275           NA          254         2506 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
          NA         2268         1310         1882         1631         1359 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
        1674         1574         1372         1199         1093         1117 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
        1095          804          672          792          419         1089 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
         796         2792           NA         1434         1606          125 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
         154           85          182          170          821          526 
TCGA-QG-A5Z2 
         449 
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=78,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=277,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=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=20,	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 439 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=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  10  77 300  50 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   11    77   300    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  10  77 300  50 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   11    77   300    50 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
260 101  77 
[1] "table(vv)"
vv
 N0  N1  N2 
260 101  77 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
260 101  77 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
260 101  77 
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       T0+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
  T0+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       T0+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
  T0+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  29   4
  subtype2 116  31
  subtype3 143  38
  subtype4  41  11
subtype1 subtype2 subtype3 subtype4 
      33      147      181       52 
subtype1 subtype2 subtype3 subtype4 
       4       31       38       11 
$subtype1
TCGA-3L-AA1B TCGA-A6-4107 TCGA-AA-3552 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3851 
        5.06        32.45        13.02        50.04         5.03        33.07 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3968 TCGA-AA-A004 TCGA-AA-A00Z TCGA-AA-A01X 
       12.99        24.00        21.99        13.94        21.99        26.01 
TCGA-AA-A029 TCGA-AD-A5EK TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4684 TCGA-AZ-6607 
       51.98         0.43         5.19         5.52        65.00         3.19 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-5341 
        2.24         2.14         3.29         1.35         8.02        29.06 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6165 TCGA-CM-6677 TCGA-D5-5537 TCGA-DM-A1D8 
       15.02        15.02        16.04        11.08        14.99        12.59 
TCGA-F4-6855 TCGA-G4-6307 TCGA-NH-A50T 
       35.41        55.04         4.11 

$subtype2
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        43.43        17.79        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       45.60        15.52        34.65        36.53        14.53        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-A6-6654 TCGA-A6-6782 
       24.13        25.08        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         5.03         6.97        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       34.03        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 
       24.00        19.99        13.94        19.99         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3841 
       14.01        15.02        37.05        19.00        85.05        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        29.98         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       26.01        27.02         7.96        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        17.03        14.99        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       12.00        31.00        33.04         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       41.00        40.96         4.21         1.02         0.10         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-4682 
       14.50        16.31         0.95        15.75        75.25        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5914 
       29.56         5.23         1.94         0.07        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        2.01         8.02        13.02        22.03        16.01         5.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5538 
       17.03        14.04        29.03        15.02        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       19.59        13.51        18.25         1.32        15.12        17.13 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1HA 
       13.41        11.38       130.65        92.75        13.32       131.51 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6808 
       26.47       119.93        35.97         8.61        13.38        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
        1.28         0.53        28.21         8.35        82.39        61.87 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       44.68        45.11        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50V TCGA-QG-A5YV 
       46.75         5.06        26.99 

$subtype3
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       46.65        43.76        23.38        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       16.04        31.63        33.53        22.09        22.06         8.38 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.16        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       24.92         1.02         3.02        35.01        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       13.02         1.02        24.03        37.05         8.05        19.07 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
       29.00         0.99        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 
        6.97        54.02         0.92        47.05        11.01        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3864 
        1.02        17.98        15.95        38.99        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 
       31.00        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-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R 
       38.07         1.02        35.01        35.01        39.06        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
        0.72         0.76         0.46         0.92        27.09         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       21.44        17.82        50.37        58.39         1.41        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-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.06         3.25         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      102.44        40.34        70.16        51.32        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        13.05        11.01        12.03        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 
       17.75         7.92        17.85        12.49        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       24.43        49.91       140.38       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       14.04        81.37        60.79        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       13.64        13.45         6.18        35.87         1.55        29.59 
TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       16.24        19.43       107.67        23.51        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       53.62        51.75        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA 
       35.80        26.17        47.15        52.80         2.79         5.98 
TCGA-QG-A5Z2 
       14.76 

$subtype4
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       27.09        25.18         9.63         1.02        37.05         1.02 
TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3558 TCGA-AA-3660 
        1.02        36.03        19.07        26.01        20.98        78.08 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3858 TCGA-AA-3875 TCGA-AA-3979 
       47.01         5.98        36.00        31.07        18.05        24.00 
TCGA-AA-A00K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O TCGA-AD-6899 
       18.05         1.02        37.02         5.03         0.92         1.58 
TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6606 TCGA-CK-4952 TCGA-CM-5348 
        5.65        83.80        62.79        11.74        15.62        22.98 
TCGA-CM-5349 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5541 
       30.08        21.99        13.02        11.01        11.08        11.51 
TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
        4.50        15.58         7.53        10.13        12.43         9.04 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H 
      119.70        38.20         7.50        44.32         6.12       117.07 
TCGA-F4-6805 TCGA-G4-6311 TCGA-NH-A6GB TCGA-QG-A5YX 
       16.31        39.42         5.59        17.29 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.07     0.07     0.92 
subtype1 subtype2 subtype3 subtype4 
   65.00   131.51   140.38   119.70 
subtype1 subtype2 subtype3 subtype4 
   13.94    21.01    21.01    16.80 
[1] "0.4 - 65.0 (13.9)"  "0.1 - 131.5 (21.0)" "0.1 - 140.4 (21.0)"
[4] "0.9 - 119.7 (16.8)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       7        0        2        13         0         0         2
  subtype2      19        0        5        34         2         1         5
  subtype3      35        1       15        70         6         0         9
  subtype4      11        0        6        10         0         0         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          2          2          1        3         3         0
  subtype2          6         25         16       26         8         0
  subtype3          3         20         16        8         3         1
  subtype4          2          6          5        5         2         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           7       19       35       11
  STAGE IA          0        0        1        0
  STAGE II          2        5       15        6
  STAGE IIA        13       34       70       10
  STAGE IIB         0        2        6        0
  STAGE IIC         0        1        0        0
  STAGE III         2        5        9        5
  STAGE IIIA        2        6        3        2
  STAGE IIIB        2       25       20        6
  STAGE IIIC        1       16       16        5
  STAGE IV          3       26        8        5
  STAGE IVA         3        8        3        2
  STAGE IVB         0        0        1        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1  T2  T3  T4
  subtype1     0   9  24   3
  subtype2     5  23 108  15
  subtype3     5  33 127  25
  subtype4     1  11  35   5
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        0        5        5        1
  T2           9       23       33       11
  T3          24      108      127       35
  T4           3       15       25        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  23   8   5
  subtype2  68  48  34
  subtype3 131  32  28
  subtype4  30  13   9
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       23       68      131       30
  N1        8       48       32       13
  N2        5       34       28        9
[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  25   4   2   0   4
  subtype2 103  31   3   0  12
  subtype3 153   9   1   1  23
  subtype4  39   6   1   0   6
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        25      103      153       39
  M1         4       31        9        6
  M1A        2        3        1        1
  M1B        0        0        1        0
  MX         4       12       23        6
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 19 17
  subtype2 66 85
  subtype3 94 97
  subtype4 24 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   17
  subtype2   66   85
  subtype3   94   97
  subtype4   24   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       66       94       24
  MALE         17       85       97       28
[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"
D3V8, binary
          cls
clus         0   1
  subtype1  36   0
  subtype2 147   3
  subtype3 143  47
  subtype4  47   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    0
  subtype2  147    3
  subtype3  143   47
  subtype4   47    5
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                36      147      143       47
  COLON MUCINOUS ADENOCARCINOMA        0        3       47        5
[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"
D3V9, binary
          cls
clus         0   1
  subtype1   1  35
  subtype2   1 150
  subtype3   0 191
  subtype4   1  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   35
  subtype2    1  150
  subtype3    0  191
  subtype4    1   51
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        0        1
  YES       35      150      191       51
[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  26   0   2   5
  subtype2 102   1  15   5
  subtype3 142   2   3  12
  subtype4  35   0   4   2
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       26      102      142       35
  R1        0        1        2        0
  R2        2       15        3        4
  RX        5        5       12        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         5
  subtype2                                0     1                        11
  subtype3                                1     6                        21
  subtype4                                0     0                         4
          vv
clus       WHITE
  subtype1    14
  subtype2    75
  subtype3    94
  subtype4    28
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   4        1        6        0
  BLACK OR AFRICAN AMERICAN               5       11       21        4
  WHITE                                  14       75       94       28
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 86 25
  subtype2 71 18
  subtype3 57 14
subtype1 subtype2 subtype3 
     111       89       71 
subtype1 subtype2 subtype3 
      25       18       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 
        4.11        26.99        17.29 

$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        21.01         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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
        5.06         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 
   22.03    17.56    15.58 
[1] "0.1 - 140.4 (22.0)" "0.1 - 135.7 (17.6)" "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        31         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          5         18          8       10        10         0
  subtype2          2         12          8        4         3         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        31       29       28
  STAGE IIB         1        3        1
  STAGE IIC         1        0        0
  STAGE III         3        4        0
  STAGE IIIA        5        2        3
  STAGE IIIB       18       12       11
  STAGE IIIC        8        8        7
  STAGE IV         10        4        6
  STAGE IVA        10        3        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       T0+T1 T2 T3 T4
  subtype1     3 19 79 12
  subtype2     3 18 58 11
  subtype3     1  5 54 11
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        3        3        1
  T2          19       18        5
  T3          79       58       54
  T4          12       11       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 31 18
  subtype2 57 19 15
  subtype3 42 19 10
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       63       57       42
  N1       31       19       19
  N2       18       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 19
  subtype2 63  5   1   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        1        1
  M1B        0        1        0
  MX        19       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 67
  subtype2 51 40
  subtype3 29 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   67
  subtype2   51   40
  subtype3   29   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       46       51       29
  MALE         67       40       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 107   6
  subtype2  76  15
  subtype3  59  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107    6
  subtype2   76   15
  subtype3   59   12
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA               107       76       59
  COLON MUCINOUS ADENOCARCINOMA        6       15       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   2 111
  subtype2   0  91
  subtype3   1  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  111
  subtype2    0   91
  subtype3    1   70
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        1
  YES      111       91       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 70  0  3  9
  subtype2 59  2  1 10
  subtype3 47  0  0  4
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       70       59       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                        16
  subtype2                                0     2                        13
  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              16       13       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 
       21.01       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       T0+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
  T0+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        21.01       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       T0+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
  T0+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 33  1
  subtype2 81 30
  subtype3 55 16
  subtype4 71 15
  subtype5 88 23
subtype1 subtype2 subtype3 subtype4 subtype5 
      34      111       71       86      111 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1       30       16       15       23 
$subtype1
TCGA-A6-2675 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-A565 TCGA-AA-3495 
       43.43        27.09        25.18        24.16        16.24        37.05 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 
       58.03         6.97        37.05        37.05        85.05        19.04 
TCGA-AA-3819 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3862 TCGA-AA-3956 TCGA-AA-3970 
       25.02        33.07        32.05        30.05        34.03        36.03 
TCGA-AA-3971 TCGA-AD-6548 TCGA-AZ-4684 TCGA-CK-4947 TCGA-CK-4950 TCGA-CM-4751 
       16.08        21.37        65.00        17.56        40.34        27.02 
TCGA-CM-6163 TCGA-CM-6172 TCGA-D5-5539 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6931 
       14.04        11.01        19.59        12.49        12.39        12.00 
TCGA-G4-6293 TCGA-G4-6321 TCGA-G4-6625 TCGA-G4-6627 
      107.67        22.09        91.79        47.15 

$subtype2
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       17.79        13.94        14.53        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6652 
       23.61        32.71        29.16        24.13        20.61        24.69 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3509 TCGA-AA-3514 
       61.84        52.44         1.02         1.02        62.96         1.02 
TCGA-AA-3517 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3561 TCGA-AA-3660 
       38.99        19.07        29.00        26.01        13.94        78.08 
TCGA-AA-3662 TCGA-AA-3696 TCGA-AA-3955 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-A00L 
        6.05         5.03        20.98        13.05        26.01        17.03 
TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J 
       27.02        31.00         1.02        26.01        39.98         5.03 
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-AU-3779 TCGA-AY-5543 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-5403 
        0.43        14.50        15.75         5.19        22.36        62.79 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       29.56         1.94         2.14         3.29         0.07         0.26 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5862 
      102.44        48.20        21.99         8.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6170 
       15.02        17.03        15.02        29.03        21.99        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       11.08        11.01        14.99        13.51        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 
        1.32         4.50        17.13        12.43        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
       11.38       119.70        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       12.59       140.38        44.32       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6303 
       13.38        33.67         0.53        28.21        23.51        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       44.68        55.04        45.11        36.72        36.00        46.75 
TCGA-NH-A50T TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11        26.99        17.29 

$subtype3
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3808 TCGA-A6-5657 TCGA-A6-5664 
       37.05        37.25        16.04        33.34        31.63        22.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       22.52        25.08        21.76        23.87        19.66        20.28 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3870 TCGA-AA-A01P TCGA-AD-5900 
       24.92         9.63         1.02        29.98        38.07         0.07 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AY-6196 TCGA-AZ-4323 
        1.58         1.02         0.76         0.46         0.20         1.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
       12.10       100.01         5.23         3.19         0.33         0.10 
TCGA-CA-6719 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        1.35        21.01         2.01        22.98        30.08        16.01 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6677 
       12.00        16.04        14.99        12.99        13.02        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6541 
       10.06        12.26        20.19        17.75         7.92        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-F4-6461 
        7.53        10.13         9.04         9.44        11.64        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       16.24         1.28        35.41         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6628 TCGA-NH-A50V 
       43.07        39.42        35.93        52.80         5.06 

$subtype4
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       33.53        22.06         8.38        24.39        20.12         3.02 
TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3655 
       35.01         1.02         8.05         0.99        29.95        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 
        6.97        54.02         1.02        36.03        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01Z 
       33.01        24.00        27.02        18.05         4.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 
       39.06        51.98         0.92        39.98        18.05        56.55 
TCGA-AD-6895 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
        0.72         0.92        27.09        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         5.65        32.94         5.13        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CK-4951 
        6.77        11.74         2.24         3.06         3.25        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       15.62        51.32         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       37.02        15.02        15.02        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6930 
       12.03        20.42        15.12        17.85        16.14         1.51 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       10.26        24.43        49.91         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6806 TCGA-F4-6856 
        7.76        14.04        98.24        95.18        29.59        19.43 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       53.62        51.75        26.43        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-QG-A5Z2 
       26.17        14.76 

$subtype5
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       35.11        45.60        15.52        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3516 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       32.45         5.03        13.02         9.07        24.03        36.03 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       19.07        34.03        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       21.01        13.02        24.00        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       19.99         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-3710 
       15.02        11.01         5.98        19.00        36.00        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 
        0.99         0.99        35.05        33.04         0.99        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
        0.99         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       27.02        18.05         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3977 
        2.01         2.01        21.99        50.99        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       24.00        27.02        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q 
       38.04        19.00        30.02        34.03        18.05        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q 
       15.02         0.99        32.02        12.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R 
       35.01        33.04        35.01         2.96         2.01        22.03 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4681 TCGA-CM-4748 
       40.96        16.31         0.95        75.25        83.80        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        8.02        13.02        29.06 

subtype1 subtype2 subtype3 subtype4 subtype5 
    6.97     0.07     0.07     0.72     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.67   140.38   100.01   135.65    83.80 
subtype1 subtype2 subtype3 subtype4 subtype5 
  27.055   20.610   13.640   20.930   22.030 
[1] "7.0 - 107.7 (27.1)" "0.1 - 140.4 (20.6)" "0.1 - 100.0 (13.6)"
[4] "0.7 - 135.7 (20.9)" "0.9 - 83.8 (22.0)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1       6        0        2        10         0         0         4
  subtype2      18        0        4        31         0         1         3
  subtype3       7        0        3        25         1         0         2
  subtype4      21        1       10        32         4         0         3
  subtype5      19        0        8        32         4         0         9
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          3          4          2        1         3         0
  subtype2          4         17          8       15         8         0
  subtype3          2         10          9        8         3         0
  subtype4          0         11          3        2         1         1
  subtype5          4         11         14       16         1         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       18        7       21       19
  STAGE IA          0        0        0        1        0
  STAGE II          2        4        3       10        8
  STAGE IIA        10       31       25       32       32
  STAGE IIB         0        0        1        4        4
  STAGE IIC         0        1        0        0        0
  STAGE III         4        3        2        3        9
  STAGE IIIA        3        4        2        0        4
  STAGE IIIB        4       17       10       11       11
  STAGE IIIC        2        8        9        3       14
  STAGE IV          1       15        8        2       16
  STAGE IVA         3        8        3        1        1
  STAGE IVB         0        0        0        1        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       T0+T1 T2 T3 T4
  subtype1     1  6 25  3
  subtype2     2 24 75 13
  subtype3     1  6 51 14
  subtype4     3 18 60  8
  subtype5     4 21 83 11
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        1        2        1        3        4
  T2           6       24        6       18       21
  T3          25       75       51       60       83
  T4           3       13       14        8       11
[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 22 10  3
  subtype2 62 35 16
  subtype3 37 18 17
  subtype4 68 13  9
  subtype5 65 25 29
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       22       62       37       68       65
  N1       10       35       18       13       25
  N2        3       16       17        9       29
[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 29  2   1   0  3
  subtype2 73 19   4   0 17
  subtype3 50 10   1   0  9
  subtype4 72  3   0   1 13
  subtype5 99 16   1   0  0
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        29       73       50       72       99
  M1         2       19       10        3       16
  M1A        1        4        1        0        1
  M1B        0        0        0        1        0
  MX         3       17        9       13        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"
D7V7, binary
          cls
clus        0  1
  subtype1 11 24
  subtype2 53 61
  subtype3 30 42
  subtype4 42 48
  subtype5 66 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   24
  subtype2   53   61
  subtype3   30   42
  subtype4   42   48
  subtype5   66   53
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       11       53       30       42       66
  MALE         24       61       42       48       53
[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"
D7V8, binary
          cls
clus         0   1
  subtype1  33   2
  subtype2 112   2
  subtype3  59  13
  subtype4  62  28
  subtype5 106  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    2
  subtype2  112    2
  subtype3   59   13
  subtype4   62   28
  subtype5  106   11
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                33      112       59       62      106
  COLON MUCINOUS ADENOCARCINOMA        2        2       13       28       11
[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"
D7V9, binary
          cls
clus         0   1
  subtype1   1  34
  subtype2   1 113
  subtype3   1  71
  subtype4   0  90
  subtype5   0 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   34
  subtype2    1  113
  subtype3    1   71
  subtype4    0   90
  subtype5    0  119
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        1        1        0        0
  YES       34      113       71       90      119
[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  27   1   1   2
  subtype2  68   0   8   7
  subtype3  50   0   1   6
  subtype4  60   1   0   9
  subtype5 100   1  13   0
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       27       68       50       60      100
  R1        1        0        0        1        1
  R2        1        8        1        0       13
  RX        2        7        6        9        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"
D7V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                0     4                        12
  subtype3                                1     3                        10
  subtype4                                0     4                         9
  subtype5                                0     0                         3
          vv
clus       WHITE
  subtype1    18
  subtype2    72
  subtype3    54
  subtype4    51
  subtype5    18
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        4        3        4        0
  BLACK OR AFRICAN AMERICAN               2       12       10        9        3
  WHITE                                  18       72       54       51       18
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  59  15
  subtype2  75  20
  subtype3  65  21
  subtype4 100  22
  subtype5  29   7
subtype1 subtype2 subtype3 subtype4 subtype5 
      74       95       86      122       36 
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       20       21       22        7 
$subtype1
TCGA-A6-2675 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       43.43        37.05        37.25        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       23.61        22.09        29.16        22.52        25.08        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       23.87        20.28        61.84        52.44         9.63         1.02 
TCGA-AA-3511 TCGA-AA-A01X TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6901 TCGA-AM-5820 
        6.97        26.01        21.37         1.58         1.02         0.46 
TCGA-AZ-4323 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6719 
        1.41        62.79        29.56         5.23         0.33         1.35 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
        2.01        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       17.03        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       13.02        15.02        10.06        12.26        13.51        11.51 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       17.75         7.92         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
        9.04        11.38        26.47         8.61        13.38        13.64 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6297 
       16.31        16.24         1.28         0.53        35.41        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       23.51        43.07        61.87        45.11        39.42        35.93 
TCGA-G4-6625 TCGA-G4-6627 
       91.79        47.15 

$subtype2
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       13.94        14.53        32.91        32.71        27.09        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3495 
       25.18        20.61        24.69        20.12        24.92        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3526 TCGA-AA-3655 TCGA-AA-3660 
        1.02        58.03        62.96        19.07        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-A01Z TCGA-AA-A02K TCGA-AA-A02Y 
        6.05        37.05        85.05        37.02        14.01        39.98 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        4.21         0.79         0.10         0.20         0.43        14.50 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-4684 
       15.75        17.82         5.19        58.39        22.36        65.00 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
        1.94         2.14         3.29         0.07         0.26        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4747 
      102.44        48.20        21.99         2.93       124.27         8.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       15.02        15.02        21.99        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       11.01        14.99        20.19        18.25         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A0XF 
        4.50        17.13        15.58        13.41       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6294 
       60.79       117.07        95.18        33.67       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
        8.35        53.62        44.68        55.04        36.72        36.00 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX 
       46.75         4.11         5.06        26.99        17.29 

$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        21.01        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-A288 TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
      135.65        14.04        98.24        11.11        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 
       35.87         1.55        29.59        19.43        74.56        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-QG-A5Z2 
       52.80        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 
    0.33     0.07     0.07     0.92     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
   91.79   140.38   135.65    83.80    54.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   16.67    20.61    16.19    24.00    23.69 
[1] "0.3 - 91.8 (16.7)"  "0.1 - 140.4 (20.6)" "0.1 - 135.7 (16.2)"
[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       8        0        3        23         1         0         2
  subtype2      15        0        7        30         1         1         3
  subtype3      18        1        4        29         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         15          6        6         6         0
  subtype2          3         14          4        7         8         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           8       15       18       26        4
  STAGE IA          0        0        1        0        0
  STAGE II          3        7        4        8        5
  STAGE IIA        23       30       29       34       14
  STAGE IIB         1        1        1        2        4
  STAGE IIC         0        1        0        0        0
  STAGE III         2        3        4        8        4
  STAGE IIIA        2        3        3        5        0
  STAGE IIIB       15       14        9       10        5
  STAGE IIIC        6        4       10       16        0
  STAGE IV          6        7        5       22        2
  STAGE IVA         6        8        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       T0+T1 T2 T3 T4
  subtype1     1  9 54 10
  subtype2     2 17 66 12
  subtype3     3 16 58 10
  subtype4     4 29 88 11
  subtype5     1  4 28  6
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        1        2        3        4        1
  T2           9       17       16       29        4
  T3          54       66       58       88       28
  T4          10       12       10       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 36 26 12
  subtype2 62 23 11
  subtype3 55 17 16
  subtype4 73 29 30
  subtype5 28  6  5
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       36       62       55       73       28
  N1       26       23       17       29        6
  N2       12       11       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  51   9   3   0  11
  subtype2  65  11   3   0  17
  subtype3  64   6   0   1  14
  subtype4 107  22   1   0   0
  subtype5  36   2   0   0   0
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        51       65       64      107       36
  M1         9       11        6       22        2
  M1A        3        3        0        1        0
  M1B        0        0        1        0        0
  MX        11       17       14        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 33 41
  subtype2 43 54
  subtype3 38 50
  subtype4 64 68
  subtype5 24 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   41
  subtype2   43   54
  subtype3   38   50
  subtype4   64   68
  subtype5   24   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       33       43       38       64       24
  MALE         41       54       50       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  68   6
  subtype2  91   6
  subtype3  68  20
  subtype4 122   8
  subtype5  23  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    6
  subtype2   91    6
  subtype3   68   20
  subtype4  122    8
  subtype5   23   16
                               clus
vv                              subtype1 subtype2 subtype3 subtype4 subtype5
  COLON ADENOCARCINOMA                68       91       68      122       23
  COLON MUCINOUS ADENOCARCINOMA        6        6       20        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   2  72
  subtype2   1  96
  subtype3   0  88
  subtype4   0 132
  subtype5   0  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   72
  subtype2    1   96
  subtype3    0   88
  subtype4    0  132
  subtype5    0   39
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        1        0        0        0
  YES       72       96       88      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  53   0   0   5
  subtype2  53   0   2  10
  subtype3  54   2   1   9
  subtype4 110   1  19   0
  subtype5  35   0   1   0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       53       53       54      110       35
  R1        0        0        2        1        0
  R2        0        2        1       19        1
  RX        5       10        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     2                        11
  subtype2                                0     4                        11
  subtype3                                1     5                        10
  subtype4                                0     0                         4
  subtype5                                0     0                         0
          vv
clus       WHITE
  subtype1    58
  subtype2    68
  subtype3    67
  subtype4    15
  subtype5     5
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   2        4        5        0        0
  BLACK OR AFRICAN AMERICAN              11       11       10        4        0
  WHITE                                  58       68       67       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 128  30
  subtype2  52  14
  subtype3 129  36
subtype1 subtype2 subtype3 
     158       66      165 
subtype1 subtype2 subtype3 
      30       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        21.01 
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        55         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          5         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        55       21       44
  STAGE IIB         2        0        6
  STAGE IIC         1        0        0
  STAGE III         7        2       12
  STAGE IIIA        5        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       T0+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
  T0+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 104  29
  subtype2  41   9
  subtype3  59  15
  subtype4 105  27
subtype1 subtype2 subtype3 subtype4 
     133       50       74      132 
subtype1 subtype2 subtype3 subtype4 
      29        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        21.01         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        49         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          4         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        49       19       19       33
  STAGE IIB         4        0        0        4
  STAGE IIC         1        0        0        0
  STAGE III         6        1        4       10
  STAGE IIIA        4        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       T0+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
  T0+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 61 16
  subtype2 62 15
  subtype3 50 13
subtype1 subtype2 subtype3 
      77       77       63 
subtype1 subtype2 subtype3 
      16       15       13 
$subtype1
TCGA-A6-2675 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       43.43        30.44        29.19        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6652 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3660 
       24.13        20.61        24.69         1.02         6.97        78.08 
TCGA-AA-3662 TCGA-AA-3697 TCGA-AD-6890 TCGA-AD-6965 TCGA-AU-3779 TCGA-AZ-6603 
        6.05        85.05         0.79         0.20        14.50        29.56 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 
        1.94         3.29         0.07         0.26         1.35        48.20 
TCGA-CK-5914 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6169 
       21.99        16.01         5.03        15.02        15.02        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       15.02        11.08        11.01        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6541 
       11.51        20.19        18.25         1.32        17.13        15.58 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
        7.50        44.32       131.51       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6808 
      119.93        35.97        60.79       117.07         8.61        33.67 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 
       35.41       107.67        28.21        82.39        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        39.42        36.72        36.00 

$subtype2
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       14.53        33.53        22.06        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 
       19.66        61.02         6.97        19.04         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AM-5821 TCGA-AU-6004 
        4.21        56.55         0.72         0.10         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 
       15.75        21.44        17.82         5.13        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6718 
        6.77       100.01        11.74         2.24         3.25         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       102.44        40.34        15.62        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 
        2.93       124.27        23.05        27.02        15.02        12.00 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6537 
       14.04        11.01        13.05        20.42        15.12         4.50 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 
       12.49        16.14        12.39         9.44        11.64        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-DM-A280 
       10.26        24.43        92.75        49.91       135.65         7.76 
TCGA-DM-A288 TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6856 
       14.04        98.24        95.18         6.18        29.59        19.43 
TCGA-G4-6295 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
        8.35        53.62        51.75        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        52.80 

$subtype3
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6141 
       32.91        31.63        23.61        22.09        29.16         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       25.08        24.16        21.76        23.87        20.28         1.02 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AY-6196 TCGA-AZ-4323 
        1.58         1.02         0.76         0.46         0.20         1.41 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-6717 
       62.79        12.10         5.23         3.19         3.06         0.33 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-5868 
        2.01        22.03        22.98        30.08        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6531 
       12.95        11.08        10.06        12.03        19.59        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6930 TCGA-DM-A285 TCGA-F4-6460 
        7.92        17.85         7.53         1.51         6.12        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.64        13.45        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6310 
       16.24         1.28         0.53        23.51        43.07        45.11 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6627 
       35.93        26.43        47.15 

subtype1 subtype2 subtype3 
    0.07     0.07     0.20 
subtype1 subtype2 subtype3 
  140.38   135.65    62.79 
subtype1 subtype2 subtype3 
   20.61    19.43    14.99 
[1] "0.1 - 140.4 (20.6)" "0.1 - 135.7 (19.4)" "0.2 - 62.8 (15.0)" 
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        0        3        26         0         1         4
  subtype2      15        1        5        28         2         0         2
  subtype3       5        0        2        20         1         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4         10          8        6         3         0
  subtype2          3         10          3        3         3         1
  subtype3          1         13          7        6         5         0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          10       15        5
  STAGE IA          0        1        0
  STAGE II          3        5        2
  STAGE IIA        26       28       20
  STAGE IIB         0        2        1
  STAGE IIC         1        0        0
  STAGE III         4        2        1
  STAGE IIIA        4        3        1
  STAGE IIIB       10       10       13
  STAGE IIIC        8        3        7
  STAGE IV          6        3        6
  STAGE IVA         3        3        5
  STAGE IVB         0        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     2 12 58  7
  subtype2     2 15 53  7
  subtype3     1  4 46 12
D11V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        2        2        1
  T2          12       15        4
  T3          58       53       46
  T4           7        7       12
[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 45 20 14
  subtype2 55 16  6
  subtype3 29 19 15
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       45       55       29
  N1       20       16       19
  N2       14        6       15
[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 59  7   2   0 10
  subtype2 55  4   1   1 16
  subtype3 40  9   2   0 10
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        59       55       40
  M1         7        4        9
  M1A        2        1        2
  M1B        0        1        0
  MX        10       16       10
[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"
D11V7, binary
          cls
clus        0  1
  subtype1 30 49
  subtype2 39 39
  subtype3 27 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   49
  subtype2   39   39
  subtype3   27   36
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       30       39       27
  MALE         49       39       36
[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 78  1
  subtype2 62 16
  subtype3 51 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78    1
  subtype2   62   16
  subtype3   51   12
                               clus
vv                              subtype1 subtype2 subtype3
  COLON ADENOCARCINOMA                78       62       51
  COLON MUCINOUS ADENOCARCINOMA        1       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"
D11V9, binary
          cls
clus        0  1
  subtype1  1 78
  subtype2  0 78
  subtype3  1 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   78
  subtype2    0   78
  subtype3    1   62
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        1
  YES       78       78       62
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 44  0  1  7
  subtype2 44  1  1 10
  subtype3 42  0  0  3
D11V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       44       44       42
  R1        0        1        0
  R2        1        1        0
  RX        7       10        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"
D11V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                         4
  subtype2                                0     4                         7
  subtype3                                1     2                         7
          vv
clus       WHITE
  subtype1    65
  subtype2    64
  subtype3    52
D11V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   4        4        2
  BLACK OR AFRICAN AMERICAN               4        7        7
  WHITE                                  65       64       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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 53 12
  subtype2 39 11
  subtype3 65 18
  subtype4 16  3
subtype1 subtype2 subtype3 subtype4 
      65       50       83       19 
subtype1 subtype2 subtype3 subtype4 
      12       11       18        3 
$subtype1
TCGA-A6-2675 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-6142 TCGA-AA-3496 TCGA-AA-3511 
       43.43        30.44        32.71        25.08         1.02         6.97 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3697 TCGA-AD-6548 TCGA-AD-6963 
       61.02        78.08         6.05        85.05        21.37         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6599 
        0.76         0.20        14.50        15.75        61.41         6.77 
TCGA-CA-5797 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-5344 
        3.29        17.56       102.44        40.34        48.20        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6165 
       30.08        16.01         5.03        15.02        14.04        16.04 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-5537 
       13.02        15.02        11.01        11.08        11.08        14.99 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       12.26        11.51        17.75        18.25        15.12         4.50 
TCGA-D5-6539 TCGA-D5-6541 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       12.49        15.58       130.65        13.32        12.59       140.38 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6806 
        6.12        26.47        81.37       119.93        35.97        29.59 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
      107.67        28.21        82.39        55.04        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 
       26.43        22.09        26.04        13.78        91.79 

$subtype2
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 
       14.53        33.53        22.06        27.09        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3713 TCGA-AD-6888 
       20.61        24.39        20.12         6.97        19.04         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6606 
       56.55         0.79        21.44        17.82        49.41        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6751 
        1.94         3.25        15.62        51.32         2.93       124.27 
TCGA-CM-4743 TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 
       23.05        14.04        13.05        20.19        20.42        16.14 
TCGA-D5-6920 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1DA 
       12.39        12.43       119.70        24.43        92.75         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K 
       44.32       135.65         7.76        14.04       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6586 
       95.18        33.67        53.62        44.68        51.75        35.80 
TCGA-G4-6588 TCGA-G4-6626 
       26.17        46.75 

$subtype3
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5667 TCGA-A6-6138 
       32.91        31.63        23.61        22.09        29.16        22.52 
TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
        8.38        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       20.28         1.02         0.07         0.72         1.58         1.02 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4616 
        0.46         0.92        27.09         0.20         1.41         5.13 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        12.10       100.01        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5916 
        2.24         3.06         0.33         0.10         1.35        21.01 
TCGA-CK-6748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
        2.01        27.02        22.98        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6678 
       12.00        29.03        14.99        12.99        12.95        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       10.06        12.03        19.59         7.92        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       10.13         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6459 TCGA-F4-6461 
       11.38        10.26        49.91       131.51         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       16.24         1.28         0.53        35.41        19.43        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6627 TCGA-G4-6628 
       43.07        61.87        45.11        47.15        52.80 

$subtype4
TCGA-A6-5660 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-6161 TCGA-CM-6166 
       29.19         0.07         0.26        21.99        15.02        21.99 
TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XF 
       13.51         1.32        17.13        14.30        13.41        38.20 
TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6460 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6314 
      139.17        60.79        13.38         8.35        23.51        35.93 
TCGA-G4-6315 
       36.72 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.79     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  140.38   135.65   131.51   139.17 
subtype1 subtype2 subtype3 subtype4 
  17.750   22.555   12.990   17.130 
[1] "0.1 - 140.4 (17.8)" "0.8 - 135.7 (22.6)" "0.1 - 131.5 (13.0)"
[4] "0.1 - 139.2 (17.1)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  subtype1      10        1        4        17         0         1         6
  subtype2       7        0        2        25         2         0         1
  subtype3      10        0        3        27         1         0         0
  subtype4       3        0        1         5         0         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  subtype1          4          9          2        4         4         0
  subtype2          1          5          3        2         1         1
  subtype3          3         13         11        6         6         0
  subtype4          0          6          2        3         0         0
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          10        7       10        3
  STAGE IA          1        0        0        0
  STAGE II          4        2        3        1
  STAGE IIA        17       25       27        5
  STAGE IIB         0        2        1        0
  STAGE IIC         1        0        0        0
  STAGE III         6        1        0        0
  STAGE IIIA        4        1        3        0
  STAGE IIIB        9        5       13        6
  STAGE IIIC        2        3       11        2
  STAGE IV          4        2        6        3
  STAGE IVA         4        1        6        0
  STAGE IVB         0        1        0        0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     2  9 48  6
  subtype2     2  9 36  4
  subtype3     1 10 58 14
  subtype4     0  3 15  2
D12V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        2        2        1        0
  T2           9        9       10        3
  T3          48       36       58       15
  T4           6        4       14        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 37 21  8
  subtype2 39  5  6
  subtype3 43 23 17
  subtype4 10  6  4
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       37       39       43       10
  N1       21        5       23        6
  N2        8        6       17        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"
          vv
clus       M0 M1 M1A M1B MX
  subtype1 43  5   2   0 14
  subtype2 39  2   1   1  7
  subtype3 58 10   2   0 12
  subtype4 14  3   0   0  3
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        43       39       58       14
  M1         5        2       10        3
  M1A        2        1        2        0
  M1B        0        1        0        0
  MX        14        7       12        3
[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"
D12V7, binary
          cls
clus        0  1
  subtype1 31 35
  subtype2 22 29
  subtype3 33 50
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   35
  subtype2   22   29
  subtype3   33   50
  subtype4   10   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       31       22       33       10
  MALE         35       29       50       10
[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"
D12V8, binary
          cls
clus        0  1
  subtype1 64  2
  subtype2 43  8
  subtype3 65 18
  subtype4 19  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64    2
  subtype2   43    8
  subtype3   65   18
  subtype4   19    1
                               clus
vv                              subtype1 subtype2 subtype3 subtype4
  COLON ADENOCARCINOMA                64       43       65       19
  COLON MUCINOUS ADENOCARCINOMA        2        8       18        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"
D12V9, binary
          cls
clus        0  1
  subtype1  0 66
  subtype2  0 51
  subtype3  2 81
  subtype4  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    0   51
  subtype3    2   81
  subtype4    0   20
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        0        2        0
  YES       66       51       81       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 44  1  1  4
  subtype2 22  0  1  5
  subtype3 53  0  0  7
  subtype4 11  0  0  4
D12V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       44       22       53       11
  R1        1        0        0        0
  R2        1        1        0        0
  RX        4        5        7        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         4
  subtype2                                0     2                         5
  subtype3                                1     5                         7
  subtype4                                0     2                         2
          vv
clus       WHITE
  subtype1    54
  subtype2    42
  subtype3    69
  subtype4    16
D12V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   1        2        5        2
  BLACK OR AFRICAN AMERICAN               4        5        7        2
  WHITE                                  54       42       69       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
