[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"        "-oTBLCA-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/BLCA-TP/11541262/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/11724834/BLCA-TP.mergedcluster.txt"

nPatients in clinical file=281, in cluster file=412, common to both=281
[1]  10 281
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
 60  64 113  41 
  1   2   3   4 
 60  64 113  41 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
112  97  51 
  1   2   3 
112  97  51 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
37 29 36  5 20 
 1  2  3  4  5 
37 29 36  5 20 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
43 38 27 19 
 1  2  3  4 
43 38 27 19 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
 71 110  75 
  1   2   3 
 71 110  75 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
71 81 61 43 
 1  2  3  4 
71 81 61 43 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
 81  72 126 
  1   2   3 
 81  72 126 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
58 72 61 45 43 
 1  2  3  4  5 
58 72 61 45 43 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
67 31 89 83 
 1  2  3  4 
67 31 89 83 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
54 32 62 46 20 56 
 1  2  3  4  5  6 
54 32 62 46 20 56 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 281 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
         678           NA         2555         3148         2991          147 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        1219           NA           NA           NA          377           NA 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
         363           NA           NA           NA           NA           NA 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
         522          170          111           NA          390           63 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
         469          873          304          864           NA           59 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
          89          700           NA           14           13           21 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
          NA           NA           NA           NA            4            2 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
           3            2            3            3           NA           NA 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
          NA           NA          219          166          158          496 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
          NA          284           77           NA         2020          560 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
         578          271         3981         3420          491          536 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
         475           55          322           NA         3767         2656 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
          67          121          238           NA          319         1529 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
         648          609           NA          252           NA         4283 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        1460           NA         1952         1264         2330         2049 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
         477         1249          933         1326           NA          796 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
         750            3           15           16           NA           18 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
          17           20           42           25          395          436 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
          37           14          392          477           NA          209 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
          NA          378          363          483         1397           NA 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
         683          186          390           NA          401           NA 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
          NA           60          699          454          455          454 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
         110          369          407         1130           NA          209 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
          NA           NA          208           NA          209         1511 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
          81          147           NA          194         1541          572 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
         283          204          125           63           81           67 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
         122          330          462          217          106          124 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
          NA          197          679         1884          931          173 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
          NA         1072          525          214           NA           26 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        1602           NA          592           88           68          481 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
         137          484          428          540           34           81 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
         235           64           95          638           67          224 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
         195          231          344           62          824          171 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
          NA           NA          134          195          187          173 
TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
         232           NA          237          126          203          195 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
         580          351           46          205         1174           93 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
          NA          250          266          105          142           76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
         197          320           53           55          130          194 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
         193          105          359          410          372          507 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
         433           NA          114         1370           NA         2705 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
        2964         1709           NA           NA           NA           NA 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
        2423           NA           NA          640           NA          799 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
          NA           68           NA         2027           64           NA 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
          NA           NA           NA         2790           NA           NA 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
          NA           NA           NA           NA         2293           NA 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
         315          147           NA          242          275 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=84,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=177,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "NUMBER.OF.LYMPH.NODES"       "RACE"                       
[11] "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 281 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, 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   1  80 137  40 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      82      137       40 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  80 137  40 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      82      137       40 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
168  28  56   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
168  28  56   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
168  28  56   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
168  28  56   7 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=60, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 38 21
  subtype2 45 18
  subtype3 72 35
  subtype4 27 14
subtype1 subtype2 subtype3 subtype4 
      59       63      107       41 
subtype1 subtype2 subtype3 subtype4 
      21       18       35       14 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-BT-A20P TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       22.29       103.50        17.88         5.06         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.67        15.42         9.99        23.01         2.14        66.41 
TCGA-DK-A1AB TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.91        10.59        87.32        50.27        17.98        64.18 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SS 
       30.67        43.59         8.94        45.93        12.82         1.97 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O 
        3.62        13.38         5.36        27.45        49.68         4.83 
TCGA-FD-A62S TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
        6.38         3.25         6.48        35.24        17.26        20.12 
TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R 
       52.67         2.24        14.07        20.98         2.20        11.31 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HQ 
        6.41         7.63         7.79         6.67         6.41         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-XF-A8HB TCGA-XF-A8HD 
       38.60         3.06         9.01         4.67        45.04        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-AAMW TCGA-YF-AA3M 
       56.19        15.35         1.87         8.32         9.04 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20W 
       11.97         4.83        40.08         2.66        32.84         8.35 
TCGA-BT-A2LA TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A0YR TCGA-CU-A3KJ 
       17.16        28.70         8.98         0.43         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A3IK TCGA-DK-A3IL 
        5.19        18.41       130.88       112.44         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
        7.82         8.22        48.00        67.36        15.68        41.06 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV 
       15.35        26.17         0.49         0.59         0.56         1.22 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BY TCGA-FD-A5C0 
       24.30        19.79        22.98        14.93         6.84         6.87 
TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF 
        6.28         9.30         2.66        15.19         4.08        61.94 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42P 
        0.85        19.46         4.50         1.12         7.73         6.41 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G TCGA-K4-A6MB 
        4.73         4.41         5.69         4.14        19.07         4.27 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HC TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T6 
       13.48        12.23         6.58        28.24        26.27         2.10 
TCGA-XF-AAML TCGA-XF-AAMX TCGA-YF-AA3L 
        7.63         6.77         7.96 

$subtype3
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       84.00        98.33         7.33        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        19.50        14.89        14.96         8.25 
TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        2.07        28.41         1.94         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AE 
       16.31         1.84         9.34         2.53        19.00        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
       17.62        15.62        10.49        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.55       140.81        41.56        76.60        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.53         0.66         1.38         0.82        14.33         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SP 
       15.68         4.01        12.43        15.88         6.12        13.18 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        14.96        14.93        12.13        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK 
        6.87         5.69        50.66        18.81         4.01        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        7.13         3.48        30.61         5.69        26.93         7.04 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A76B 
        6.94         2.89        17.75         2.66         3.12         7.36 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-AATO TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS 
        7.59        27.09        10.65        11.54         1.51         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX 
        3.45         2.50         6.38        11.80        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9T2 
        3.75        97.45        17.88        64.80        11.90        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN4 
       16.27        66.64        92.98        91.73        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39         3.88        10.36         4.83         0.66 

$subtype4
TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-DK-A2HX TCGA-DK-A2I2 
        6.74         5.06        12.82        12.92         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IV TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 
      123.85         9.67        12.99        12.89         6.87        11.93 
TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       22.45         5.52         2.66         6.71         4.11         2.07 
TCGA-FD-A6TH TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GD-A3OP TCGA-GU-A762 TCGA-GU-A766 
        2.20        15.81        15.91         2.10         2.04         5.62 
TCGA-GV-A3JX TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        6.15         8.22         6.48        10.52         1.74         1.81 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY 
        6.35         3.45        16.67        79.66        23.64        21.04 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 
        2.24        10.82        54.90         2.96        56.48 

subtype1 subtype2 subtype3 subtype4 
    1.87     0.43     0.07     1.74 
subtype1 subtype2 subtype3 subtype4 
  103.50   130.88   140.81   123.85 
subtype1 subtype2 subtype3 subtype4 
   10.59     7.82    10.85     6.87 
[1] "1.9 - 103.5 (10.6)" "0.4 - 130.9 (7.8)"  "0.1 - 140.8 (10.8)"
[4] "1.7 - 123.8 (6.9)" 
D1V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       20        18       21
  subtype2        0       1       16        18       28
  subtype3        1       1       38        45       26
  subtype4        0       0       12        12       17
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE 0A         0        0        1        0
  STAGE I          0        1        1        0
  STAGE II        20       16       38       12
  STAGE III       18       18       45       12
  STAGE IV        21       28       26       17
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       19 29  5
  subtype2       17 34  9
  subtype3       36 50 19
  subtype4       10 23  6
D1V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       19       17       36       10
  T3             29       34       50       23
  T4              5        9       19        6
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 31  9  9  1
  subtype2 33  8 18  2
  subtype3 82  9 14  2
  subtype4 20  2 14  2
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31       33       82       20
  N1        9        8        9        2
  N2        9       18       14       14
  N3        1        2        2        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       M0 M1 MX
  subtype1 27  1 32
  subtype2 30  1 32
  subtype3 58  3 52
  subtype4 14  2 25
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       27       30       58       14
  M1        1        1        3        2
  MX       32       32       52       25
[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 35
  subtype2 13 51
  subtype3 26 87
  subtype4 13 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   35
  subtype2   13   51
  subtype3   26   87
  subtype4   13   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       13       26       13
  MALE         35       51       87       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"
D1V8, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         4    46
  subtype2     6                         2    51
  subtype3    19                         6    83
  subtype4     4                         1    35
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        6       19        4
  BLACK OR AFRICAN AMERICAN        4        2        6        1
  WHITE                           46       51       83       35
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus         0   1
  subtype1   3  50
  subtype2   1  59
  subtype3   1 109
  subtype4   0  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   50
  subtype2    1   59
  subtype3    1  109
  subtype4    0   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        1        0
  NOT HISPANIC OR LATINO       50       59      109       40
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 77 34
  subtype2 69 26
  subtype3 29 17
subtype1 subtype2 subtype3 
     111       95       46 
subtype1 subtype2 subtype3 
      34       26       17 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 
       22.29        98.33         4.83         7.33        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       11.93        19.04        12.16         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        17.16         3.65        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR 
       28.41         1.94         2.93         0.43        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2I1 
        5.46         9.34         2.53       130.88        17.62        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       123.85        87.32         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7DV TCGA-E7-A7XN 
       15.68        41.06        43.59        24.66         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        45.93        24.30         6.12         5.52        13.18 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96        14.93        12.13        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        6.87         5.69        49.68         2.66         6.28         6.38 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EF 
       18.81         6.71         2.07        10.85         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GC-A3YS 
       30.61         5.69        26.93         6.94        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A40E 
        2.66        20.98         7.59         2.04         5.62         6.41 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22         8.75         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI 
        6.48         1.74         1.81         6.38         6.35        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SI TCGA-XF-A9SX 
       16.67        14.24        88.93        97.45        79.66        23.64 
TCGA-XF-A9SZ TCGA-YC-A8S6 TCGA-YC-A9TC 
       28.24         4.83         0.66 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20W 
       11.97        84.00        40.08         6.74        32.84         8.35 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 
        5.59         4.67        15.42        28.70         8.98        23.01 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 
        0.69         0.07         0.10         5.19         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IS 
       19.00       112.44        16.14         2.20         3.98        50.27 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       17.98        64.18        41.56        67.36        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       26.17         0.49         0.53         0.59         0.56         1.38 
TCGA-E7-A6ME TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       12.99        11.93        12.82        19.79         1.97        22.98 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TA 
        3.62        13.38         5.36        27.45         4.83        50.66 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        9.30         4.11         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY 
        4.08         3.25        22.32        35.24         7.04         0.85 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A2C5 
       52.67         2.89         4.50        15.91        14.07         7.73 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JV 
        3.12         2.20         7.36         6.41        27.09         4.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
        6.15         5.69         7.63         7.79         6.67        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A6MB 
       11.54         1.51         6.74        38.60         3.06         4.27 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HF 
        3.45        11.80        13.48         3.75         6.58        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9T0 TCGA-YC-A89H TCGA-YF-AA3L 
       15.35         1.87        26.27        10.36         7.96 

$subtype3
TCGA-2F-A9KR TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F7 
      103.50         2.66        17.88        19.50        14.89         2.04 
TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.46         0.13         0.10         0.07         0.10         4.90 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2HX 
       16.31         1.84        18.41         8.91        15.62         1.81 
TCGA-DK-A3IV TCGA-DK-A6B0 TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF 
        9.67        76.60         0.10         0.66         0.82        14.33 
TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TG TCGA-FJ-A3ZE 
       22.45        46.78         6.84         6.87         2.66         3.48 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GD-A3OP TCGA-GU-A42R 
       17.26        20.12         2.24        15.81         2.10        11.31 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3QI TCGA-K4-A54R TCGA-S5-A6DX 
        4.73        10.65         6.41         4.14        10.52         0.85 
TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9T4 
       45.04        17.88        64.80        16.27 

subtype1 subtype2 subtype3 
    0.43     0.07     0.07 
subtype1 subtype2 subtype3 
  140.81   112.44   103.50 
subtype1 subtype2 subtype3 
    9.99     7.79     7.89 
[1] "0.4 - 140.8 (10.0)" "0.1 - 112.4 (7.8)"  "0.1 - 103.5 (7.9)" 
D2V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       28        49       34
  subtype2        1       2       35        26       31
  subtype3        0       0       21        10       19
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        1        0
  STAGE I          0        2        0
  STAGE II        28       35       21
  STAGE III       49       26       10
  STAGE IV        34       31       19
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       27 62 16
  subtype2       33 42 12
  subtype3       18 19  9
D2V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       27       33       18
  T3             62       42       19
  T4             16       12        9
[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       N0 N1 N2 N3
  subtype1 74 14 16  4
  subtype2 56 10 19  2
  subtype3 26  2 15  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       74       56       26
  N1       14       10        2
  N2       16       19       15
  N3        4        2        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       M0 M1 MX
  subtype1 48  3 61
  subtype2 48  2 46
  subtype3 32  2 17
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       48       48       32
  M1        3        2        2
  MX       61       46       17
[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 33 79
  subtype2 23 74
  subtype3 10 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   79
  subtype2   23   74
  subtype3   10   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       23       10
  MALE         79       74       41
[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, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         8    93
  subtype2    13                         5    70
  subtype3    13                         0    35
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4       13       13
  BLACK OR AFRICAN AMERICAN        8        5        0
  WHITE                           93       70       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"
D2V12, binary
          cls
clus         0   1
  subtype1   1 103
  subtype2   2  88
  subtype3   1  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  103
  subtype2    2   88
  subtype3    1   48
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        1
  NOT HISPANIC OR LATINO      103       88       48
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 27  6
  subtype2 16 12
  subtype3 19 17
  subtype4  2  3
  subtype5 10 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       28       36        5       20 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       12       17        3       10 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F6 
       40.08        17.88        19.50         4.67        28.70        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AA 
        0.46         0.69         5.19        16.31         2.53        19.00 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3X2 
      130.88       112.44        15.62        10.59         3.98        17.98 
TCGA-E7-A3Y1 TCGA-FD-A3NA TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM 
        0.10        45.93         3.48         4.08         0.85         2.89 
TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
        7.73        11.31         5.69         7.79         6.67        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        1.51         6.74        38.60 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A42B TCGA-C4-A0F0 
        7.33         6.58         5.06         8.35        15.42         1.94 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A3WY 
        8.91        17.62         1.81         2.20        21.30       140.81 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ 
       12.89        15.68         6.87         4.01        12.43        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45         6.12         5.52        46.78        19.79         1.97 
TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WU TCGA-K4-A3WV 
        2.10         4.41         3.45         4.67 

$subtype3
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T 
        2.66         6.74        19.04        32.84        12.16        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F1 
       14.96         5.06         8.25        17.16        12.82         2.93 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AE 
        2.04         0.43         5.46         2.14        66.41        16.14 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-E5-A2PC 
        7.79       123.85         8.22        20.02        48.00        43.59 
TCGA-E7-A3X6 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-G2-A2EJ TCGA-G2-A2EO 
       24.66         8.94        11.93        12.82        30.61        35.24 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI TCGA-GV-A40E 
       17.26         2.24        17.75         1.12         4.14         6.41 

$subtype4
TCGA-BT-A0YX TCGA-BT-A2LB TCGA-DK-A3IQ TCGA-G2-A2EK TCGA-GD-A3OQ 
       11.93         5.59        10.49         5.69         3.12 

$subtype5
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IM TCGA-DK-A3IV 
        3.65         2.07         8.98        12.92         7.82         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-G2-A2EC 
        8.28        10.55        15.88        13.18        15.19        22.32 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GD-A3OS TCGA-GV-A3JW 
       61.94        26.93         7.04        20.12        20.98         6.41 
TCGA-GV-A3QF TCGA-K4-A3WS 
        7.63         8.75 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     1.81     0.43     3.12     2.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.88   140.81   123.85    11.93    61.94 
subtype1 subtype2 subtype3 subtype4 subtype5 
    7.79     7.10    12.49     5.69    10.11 
[1] "0.1 - 130.9 (7.8)"  "1.8 - 140.8 (7.1)"  "0.4 - 123.8 (12.5)"
[4] "3.1 - 11.9 (5.7)"   "2.1 - 61.9 (10.1)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       12         9       12
  subtype2       0        5         8       16
  subtype3       0        8        16       11
  subtype4       0        1         3        1
  subtype5       0       10         6        4
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        0        0        0        0
  STAGE II        12        5        8        1       10
  STAGE III        9        8       16        3        6
  STAGE IV        12       16       11        1        4
[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       T0+T1+T2 T3 T4
  subtype1       10 15  4
  subtype2        6 15  8
  subtype3        8 21  5
  subtype4        0  3  1
  subtype5        3  9  1
D3V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       10        6        8        0        3
  T3             15       15       21        3        9
  T4              4        8        5        1        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20  1  9  2
  subtype2 13  4  9  2
  subtype3 23  5  4  2
  subtype4  4  1  0  0
  subtype5 11  2  2  0
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       20       13       23        4       11
  N1        1        4        5        1        2
  N2        9        9        4        0        2
  N3        2        2        2        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"
          vv
clus       M0 M1 MX
  subtype1 25  2  9
  subtype2 10  2 17
  subtype3 25  0 11
  subtype4  4  0  1
  subtype5  9  1 10
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       25       10       25        4        9
  M1        2        2        0        0        1
  MX        9       17       11        1       10
[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"
D3V7, binary
          cls
clus        0  1
  subtype1  7 30
  subtype2 10 19
  subtype3  8 28
  subtype4  2  3
  subtype5  6 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   30
  subtype2   10   19
  subtype3    8   28
  subtype4    2    3
  subtype5    6   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        7       10        8        2        6
  MALE         30       19       28        3       14
[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"
D3V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        2       10        1       10 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype5" "subtype5" "subtype1" "subtype3" "subtype5"
[13] "subtype5" "subtype3" "subtype5" "subtype3" "subtype3" "subtype5"
[19] "subtype5" "subtype1" "subtype1" "subtype3" "subtype3" "subtype5"
[25] "subtype5" "subtype1" "subtype5" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype1"
D3V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       18       22        2       13 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype5" "subtype2" "subtype3"
[13] "subtype1" "subtype1" "subtype1" "subtype5" "subtype3" "subtype1"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3" "subtype3"
[31] "subtype5" "subtype5" "subtype3" "subtype1" "subtype2" "subtype2"
[37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype5"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype5"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype5"
[55] "subtype3" "subtype5" "subtype3" "subtype5" "subtype1" "subtype3"
[61] "subtype3" "subtype1" "subtype5" "subtype1" "subtype2" "subtype1"
[67] "subtype5" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[73] "subtype1" "subtype1" "subtype1" "subtype5" "subtype2"
D3V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         1    27
  subtype2     0                         2    24
  subtype3     1                         3    29
  subtype4     0                         0     5
  subtype5     0                         3    15
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            7        0        1        0        0
  BLACK OR AFRICAN AMERICAN        1        2        3        0        3
  WHITE                           27       24       29        5       15
[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"
D3V12, binary
          cls
clus        0  1
  subtype1  0 33
  subtype2  1 25
  subtype3  1 31
  subtype4  0  5
  subtype5  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    1   25
  subtype3    1   31
  subtype4    0    5
  subtype5    0   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        1        0        0
  NOT HISPANIC OR LATINO       33       25       31        5       18
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 28 11
  subtype2 23 14
  subtype3 12 15
  subtype4 11  8
subtype1 subtype2 subtype3 subtype4 
      39       37       27       19 
subtype1 subtype2 subtype3 subtype4 
      11       14       15        8 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB 
       40.08         2.66        11.93        17.88        19.50         5.59 
TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        4.67        28.70         2.93        23.01         0.46         0.69 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        5.19        16.31         2.53         2.14        66.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      112.44        15.62        10.59        48.00        24.66         0.10 
TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY 
        8.94        45.93         6.12         4.08        20.12         0.85 
TCGA-GC-A3BM TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK 
        2.89         3.12        11.31         5.69         7.79         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE 
       19.07         1.51        38.60 

$subtype2
TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0EZ 
        7.33         5.06         8.35         3.65        15.42         8.98 
TCGA-C4-A0F0 TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK 
        1.94         8.91        17.62         1.81       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY 
        3.98         8.22        10.49        21.30        20.02       140.81 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.89        15.68         6.87        12.43        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-G2-A2EK 
       12.82         5.52        46.78        19.79         1.97         5.69 
TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WS TCGA-K4-A3WU 
        2.24         7.73         2.10         4.41         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

$subtype3
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T 
        6.74         6.58        19.04        32.84        12.16        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F7 
       14.96         5.06         8.25        17.16        12.82         2.04 
TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A3X2 TCGA-E5-A2PC 
        0.43         5.46       130.88        16.14        17.98        43.59 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        4.01        11.93        15.88        26.93        35.24        17.26 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI 
       17.75         1.12         4.14 

$subtype4
TCGA-BT-A3PK TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IV TCGA-DK-A3WW 
        2.07        12.92         7.79         7.82         9.67         8.28 
TCGA-DK-A3WX TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.55        13.18        15.19         3.48        22.32        61.94 
TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-GD-A3OS TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E 
       30.61         7.04        20.98         6.41         7.63         6.41 
TCGA-H4-A2HQ 
        6.74 

subtype1 subtype2 subtype3 subtype4 
    0.10     1.81     0.43     2.07 
subtype1 subtype2 subtype3 subtype4 
  112.44   140.81   130.88    61.94 
subtype1 subtype2 subtype3 subtype4 
    8.94     8.35    14.89     8.28 
[1] "0.1 - 112.4 (8.9)"  "1.8 - 140.8 (8.3)"  "0.4 - 130.9 (14.9)"
[4] "2.1 - 61.9 (8.3)"  
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       15        12       12
  subtype2       0        7        11       20
  subtype3       0        5        14        7
  subtype4       0        9         5        5
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        0        0        0
  STAGE II        15        7        5        9
  STAGE III       12       11       14        5
  STAGE IV        12       20        7        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       T0+T1+T2 T3 T4
  subtype1       14 16  6
  subtype2        7 22  8
  subtype3        4 18  4
  subtype4        2  7  1
D4V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       14        7        4        2
  T3             16       22       18        7
  T4              6        8        4        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"
          vv
clus       N0 N1 N2 N3
  subtype1 24  4  8  1
  subtype2 19  6 10  2
  subtype3 19  3  4  1
  subtype4  9  0  2  2
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       24       19       19        9
  N1        4        6        3        0
  N2        8       10        4        2
  N3        1        2        1        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       M0 M1 MX
  subtype1 30  1 11
  subtype2 18  2 18
  subtype3 16  0 11
  subtype4  9  2  8
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       30       18       16        9
  M1        1        2        0        2
  MX       11       18       11        8
[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"
D4V7, binary
          cls
clus        0  1
  subtype1  7 36
  subtype2 14 24
  subtype3  6 21
  subtype4  6 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   36
  subtype2   14   24
  subtype3    6   21
  subtype4    6   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       14        6        6
  MALE         36       24       21       13
[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"
D4V8, continuous
D4V9, continuous
D4V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         1    32
  subtype2     0                         1    32
  subtype3     1                         4    20
  subtype4     0                         3    16
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            7        0        1        0
  BLACK OR AFRICAN AMERICAN        1        1        4        3
  WHITE                           32       32       20       16
[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"
D4V12, binary
          cls
clus        0  1
  subtype1  0 38
  subtype2  2 31
  subtype3  0 24
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   38
  subtype2    2   31
  subtype3    0   24
  subtype4    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        0        0
  NOT HISPANIC OR LATINO       38       31       24       19
[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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 43 27
  subtype2 79 24
  subtype3 49 26
subtype1 subtype2 subtype3 
      70      103       75 
subtype1 subtype2 subtype3 
      27       24       26 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       22.29         4.83         7.33         2.66         6.74        12.39 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB 
       19.04        12.16        19.50         5.06        17.16         5.59 
TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AF 
        3.65         8.98         2.53         2.14       130.88        17.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
        1.81        10.59       123.85         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3WY TCGA-DK-A6B2 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3B8 
       20.02       140.81        15.68         1.22         4.01        12.43 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45         6.12        12.82        13.18        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96        14.93        13.38        37.15        11.01 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        5.69        27.45         6.87         2.66         6.28         6.38 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
       18.81         9.30         2.07         2.66         2.20        10.85 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GD-A3OS TCGA-GU-A762 TCGA-GU-AATO 
        6.48        35.24        15.81        20.98         2.04        10.65 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-R3-A69X 
        8.75         3.45        10.52         1.74         6.38        14.24 
TCGA-XF-A8HD TCGA-XF-A8HH TCGA-XF-A9SX TCGA-XF-A9SZ 
       88.93         1.87        23.64        28.24 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A3PH 
       11.97        84.00        40.08        17.88         8.35         4.67 
TCGA-BT-A42C TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.70        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10         0.10         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19        16.31         1.84        66.41        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV 
      112.44        15.62         2.20         3.98        50.27         9.67 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       48.00        64.18        41.56        76.60        67.36        30.67 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-FD-A3NA 
        0.66         1.38         0.82        12.99        14.33        45.93 
TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TA 
       24.30        22.98         3.62         5.36         4.83        50.66 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.11         4.01        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
        3.25        22.32         5.69        20.12         0.85         2.89 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B 
        4.50        14.07         7.73         2.10         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        6.41        11.31        27.09         4.73         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 
        4.27         3.45        11.80        13.48         0.85         3.75 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-YC-A8S6 
        6.58        56.19        15.35        17.88        64.80         4.83 
TCGA-YF-AA3L 
        7.96 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20T 
      103.50        98.33         6.58        11.93        32.84        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
       14.96         5.06         8.25        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A0YN 
       28.41         1.94         2.93         2.04         0.43        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I6 
        5.46         9.34         8.91        16.14         7.79        87.32 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-E5-A2PC 
        7.82         8.28        10.55        17.98        41.06        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.35        24.66         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43Y 
        6.87        11.93        15.88         5.52         1.97        12.13 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ 
        6.87         6.84        49.68         6.71        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC 
       26.93        17.26         7.04         6.94         2.24        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A766 
       17.75         1.12         2.66         3.12         7.59         5.62 
TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        6.41         9.01         8.22         4.67         2.50         6.48 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HB TCGA-XF-A8HE 
        1.81         6.35        12.23        16.67        45.04        97.45 
TCGA-XF-A9T4 TCGA-YC-A89H TCGA-YC-A9TC 
       16.27        10.36         0.66 

subtype1 subtype2 subtype3 
    1.22     0.07     0.43 
subtype1 subtype2 subtype3 
  140.81   112.44   103.50 
subtype1 subtype2 subtype3 
   10.75     6.67     9.01 
[1] "1.2 - 140.8 (10.8)" "0.1 - 112.4 (6.7)"  "0.4 - 103.5 (9.0)" 
D5V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       12        28       31
  subtype2        1       2       48        27       29
  subtype3        0       0       22        29       23
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        1        0
  STAGE I          0        2        0
  STAGE II        12       48       22
  STAGE III       28       27       29
  STAGE IV        31       29       23
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       11 47 12
  subtype2       46 39 11
  subtype3       19 35 14
D5V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       11       46       19
  T3             47       39       35
  T4             12       11       14
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 40  8 20  2
  subtype2 66  6 22  2
  subtype3 47 11  8  3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       40       66       47
  N1        8        6       11
  N2       20       22        8
  N3        2        2        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"
          vv
clus       M0 M1 MX
  subtype1 26  4 41
  subtype2 64  2 43
  subtype3 37  1 37
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       26       64       37
  M1        4        2        1
  MX       41       43       37
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 19 52
  subtype2 22 88
  subtype3 23 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   52
  subtype2   22   88
  subtype3   23   52
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       19       22       23
  MALE         52       88       52
[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"
D5V8, continuous
D5V9, continuous
D5V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    63
  subtype2    26                         3    75
  subtype3     2                         7    57
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1       26        2
  BLACK OR AFRICAN AMERICAN        3        3        7
  WHITE                           63       75       57
[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"
D5V12, binary
          cls
clus         0   1
  subtype1   2  65
  subtype2   1 104
  subtype3   1  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   65
  subtype2    1  104
  subtype3    1   66
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        1
  NOT HISPANIC OR LATINO       65      104       66
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 46 24
  subtype2 61 13
  subtype3 43 18
  subtype4 21 22
subtype1 subtype2 subtype3 subtype4 
      70       74       61       43 
subtype1 subtype2 subtype3 subtype4 
      24       13       18       22 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20Q 
       22.29        98.33         4.83         2.66        32.84        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F6 
        5.06        14.89         8.35         5.59         4.67        23.01 
TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        0.46         4.90         7.20         2.53         2.14        66.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK 
      130.88       112.44        17.62         1.81        10.59         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-FD-A3NA 
        3.98        10.49        21.30        48.00        15.68        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       24.30        22.45         6.12        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 
       14.93        14.96        14.93        13.38        27.45         6.87 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2EC 
       50.66         9.30         2.66         4.01        15.19        22.32 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP 
        5.69        35.24        15.81        14.07         7.73         2.10 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        4.73         4.41         5.69         8.75         3.45         2.50 
TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HF 
       10.52         4.27         6.38        14.24         0.85        56.19 
TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SZ TCGA-YC-A89H 
        1.87        64.80        28.24        10.36 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A42C TCGA-CF-A27C 
       11.97        84.00        40.08        17.88        28.70         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG 
        5.19        16.31         1.84        18.41        19.00        15.62 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       50.27         9.67        64.18        41.56        76.60        67.36 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       30.67        26.17         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.62         5.36         4.83         4.11         7.13         3.48 
TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GD-A6C6 
        4.08        20.12         0.85         2.89         4.50         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3JX 
        7.36         6.41        11.31        27.09         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.67        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.51         6.74        38.60         3.06         3.45        11.80 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HI 
       13.48         3.75        45.04         6.58        15.35        17.88 
TCGA-YC-A8S6 TCGA-YF-AA3L 
        4.83         7.96 

$subtype3
TCGA-2F-A9KR TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A3PK 
      103.50        11.93        14.96         8.25        12.82         2.07 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-CU-A0YN 
        9.99        28.41         1.94         2.93         0.43        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IM 
        5.46         9.34         8.91        16.14         7.79         7.82 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
        8.28        10.55        17.98        41.06        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       24.66         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY 
       11.93        15.88         5.52        12.13         6.87         6.84 
TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES 
       49.68         6.71         3.25        61.94        30.61        17.26 
TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        7.04         2.24        15.91        17.75         1.12         2.66 
TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A766 TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE 
        3.12         7.59         5.62         6.41         9.01         8.22 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.48         1.81         6.35        12.23        16.67        97.45 
TCGA-XF-A9T4 
       16.27 

$subtype4
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74        12.39         6.58        19.04        12.16 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-DK-A2I4 
        5.06        17.16         3.65         8.98         2.04       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WY TCGA-E7-A7DV TCGA-FD-A3B7 
       87.32         8.22        20.02       140.81         1.22         4.01 
TCGA-FD-A3B8 TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A5BS TCGA-FD-A5BT 
       12.43        12.82        13.18         1.97        37.15        11.01 
TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TF 
        5.69         2.66         6.28         6.38        18.81         2.07 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-AA3C TCGA-GD-A3OS 
        2.20        10.85         6.48        26.93         6.94        20.98 
TCGA-GU-A762 TCGA-GU-AATO TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-XF-A8HD TCGA-XF-A9SX 
        2.04        10.65         4.67         1.74        88.93        23.64 
TCGA-YC-A9TC 
        0.66 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.07     0.43     0.66 
subtype1 subtype2 subtype3 subtype4 
  130.88    84.00   103.50   140.81 
subtype1 subtype2 subtype3 subtype4 
  10.555    6.625    9.010    8.220 
[1] "0.5 - 130.9 (10.6)" "0.1 - 84.0 (6.6)"   "0.4 - 103.5 (9.0)" 
[4] "0.7 - 140.8 (8.2)" 
D6V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       13        18       39
  subtype2        1       2       44        21       11
  subtype3        0       0       17        27       16
  subtype4        0       0        8        18       17
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE 0A         0        1        0        0
  STAGE I          0        2        0        0
  STAGE II        13       44       17        8
  STAGE III       18       21       27       18
  STAGE IV        39       11       16       17
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       13 42 13
  subtype2       41 23  5
  subtype3       15 32 10
  subtype4        7 24  9
D6V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       13       41       15        7
  T3             42       23       32       24
  T4             13        5       10        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       N0 N1 N2 N3
  subtype1 31 10 27  2
  subtype2 55  2  9  1
  subtype3 41  8  6  2
  subtype4 26  5  8  2
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31       55       41       26
  N1       10        2        8        5
  N2       27        9        6        8
  N3        2        1        2        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       M0 M1 MX
  subtype1 34  2 35
  subtype2 50  2 28
  subtype3 30  0 31
  subtype4 13  3 27
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       34       50       30       13
  M1        2        2        0        3
  MX       35       28       31       27
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 19 52
  subtype2 14 67
  subtype3 20 41
  subtype4 11 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   52
  subtype2   14   67
  subtype3   20   41
  subtype4   11   32
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       14       20       11
  MALE         52       67       41       32
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
D6V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    61
  subtype2    24                         2    50
  subtype3     2                         6    48
  subtype4     1                         3    36
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2       24        2        1
  BLACK OR AFRICAN AMERICAN        2        2        6        3
  WHITE                           61       50       48       36
[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"
D6V12, binary
          cls
clus        0  1
  subtype1  0 64
  subtype2  2 77
  subtype3  0 56
  subtype4  2 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   64
  subtype2    2   77
  subtype3    0   56
  subtype4    2   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        0        2
  NOT HISPANIC OR LATINO       64       77       56       38
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 50 31
  subtype2 48 21
  subtype3 84 37
subtype1 subtype2 subtype3 
      81       69      121 
subtype1 subtype2 subtype3 
      31       21       37 
$subtype1
TCGA-2F-A9KO TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
       22.29         6.58        19.04        12.16        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B 
       14.89        14.96         8.25        17.16         5.59        15.42 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 
        1.94         0.46         0.43         4.90         9.34         2.53 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL 
        8.91        16.14        17.62         1.81       123.85         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WY TCGA-E7-A6ME TCGA-E7-A7XN TCGA-FD-A3B3 
       10.49        20.02       140.81        12.99         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ 
       15.68        12.43        24.30        22.45        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       19.79        14.96        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        6.87         5.69         6.84         2.66         6.28         6.38 
TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EC 
       18.81         2.07         2.66        10.85         6.48        22.32 
TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
        5.69        15.81        17.75         7.73         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-A767 TCGA-K4-A4AC TCGA-K4-A83P TCGA-R3-A69X 
        7.36         2.04         4.73         6.48         6.38        14.24 
TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
        1.87        79.66        11.90        23.64        21.04         2.24 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98        10.82        91.73         2.96        56.48        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 
       75.39         3.88         4.83 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97        84.00         4.83        40.08         7.33         2.66 
TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F1 
       11.93         8.35         3.65         2.07        28.70         2.93 
TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
        0.13         7.20         5.46         5.19         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV 
      130.88        10.59        87.32         2.20        21.30        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-FD-A3B7 
       67.36        15.68         1.38        14.33         1.22         4.01 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.82         1.97        22.98        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI 
        4.83        50.66         9.30         6.71         2.20         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A766 
       15.19         4.08         0.85         1.12         6.41         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.65         4.41         7.63        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LC-A66R 
       38.60         8.75         3.45         2.50         4.27         6.35 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ 
       13.48         0.85         6.58        28.24        26.27        54.90 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77         7.96         9.04 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20V 
      103.50        98.33         6.74        32.84        17.88         5.06 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        4.67        12.82         9.99        28.41         8.98        23.01 
TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        2.04         0.69         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        0.10        12.92        16.31        66.41        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
      112.44        15.62         7.79         7.82         8.22        50.27 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67         8.28        10.55        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        41.06        30.67        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 
        0.66         0.82         8.94         6.87        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       45.93         6.12         5.52        14.93        14.93         3.62 
TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF 
        5.36         4.11         7.13         3.48         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       52.67        19.46         2.89         2.24         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       14.07         2.66         3.12         2.20         7.59        11.31 
TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       27.09         6.41         6.15         5.69         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        6.67         6.41        11.54         3.06         9.01         8.22 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-LT-A8JT 
        4.67        10.52         1.74         1.81         3.45        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        16.67         3.75        45.04        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9T2 TCGA-XF-A9T4 
       56.19        15.35        17.88        64.80        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-YC-A89H 
       66.64         2.10         7.63         8.32        30.94        10.36 
TCGA-YC-A9TC 
        0.66 

subtype1 subtype2 subtype3 
    0.43     0.13     0.07 
subtype1 subtype2 subtype3 
  140.81   130.88   112.44 
subtype1 subtype2 subtype3 
   11.90     6.87     9.99 
[1] "0.4 - 140.8 (11.9)" "0.1 - 130.9 (6.9)"  "0.1 - 112.4 (10.0)"
D7V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       17        28       34
  subtype2        0       1       16        25       29
  subtype3        1       1       54        40       29
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        0        1
  STAGE I          0        1        1
  STAGE II        17       16       54
  STAGE III       28       25       40
  STAGE IV        34       29       29
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       15 51 12
  subtype2       19 36 13
  subtype3       48 49 14
D7V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       15       19       48
  T3             51       36       49
  T4             12       13       14
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 45  6 27  0
  subtype2 38 10 16  3
  subtype3 84 11 13  4
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       45       38       84
  N1        6       10       11
  N2       27       16       13
  N3        0        3        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"
          vv
clus       M0 M1 MX
  subtype1 30  2 49
  subtype2 31  1 39
  subtype3 70  4 52
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       30       31       70
  M1        2        1        4
  MX       49       39       52
[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"
D7V7, binary
          cls
clus        0  1
  subtype1 32 49
  subtype2 12 60
  subtype3 33 93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   49
  subtype2   12   60
  subtype3   33   93
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       12       33
  MALE         49       60       93
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         4    70
  subtype2     9                         3    52
  subtype3    16                         7    91
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        9       16
  BLACK OR AFRICAN AMERICAN        4        3        7
  WHITE                           70       52       91
[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"
D7V12, binary
          cls
clus         0   1
  subtype1   1  79
  subtype2   3  64
  subtype3   1 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   79
  subtype2    3   64
  subtype3    1  114
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        1
  NOT HISPANIC OR LATINO       79       64      114
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 36 22
  subtype2 45 25
  subtype3 40 15
  subtype4 31 14
  subtype5 30 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      58       70       55       45       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       25       15       14       13 
$subtype1
TCGA-2F-A9KO TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T 
       22.29         6.58        19.04        12.16        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F 
       14.96         5.06        17.16        12.82        15.42        28.41 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 
        1.94         0.43         5.46         8.91        16.14         7.79 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-E5-A2PC 
        7.82         8.22         8.28        10.55        17.98        43.59 
TCGA-E5-A4TZ TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 
       15.35        14.33         0.46         8.94         6.87        11.93 
TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-G2-A2EF 
       15.88        14.93        37.15         5.69         6.84        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GD-A3OS TCGA-GU-A42Q 
       30.61        35.24        17.26         2.24        20.98         7.59 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ 
        3.06         9.01         8.22         4.67         6.48         1.74 
TCGA-K4-A6FZ TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A9SY TCGA-XF-A9T2 
        1.81        12.23        16.67        97.45        21.04        18.90 
TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN8 
       66.64         2.96         8.32         3.88 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97        84.00         4.83        40.08         7.33         2.66 
TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
       11.93         8.35         3.65         2.07        28.70         9.99 
TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
        2.93         0.13         7.20         5.19         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 
      130.88        87.32         2.20        21.30        64.18        67.36 
TCGA-DK-A6B2 TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SO 
       15.68         1.38         1.22         4.01        12.82         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       46.78         1.97        11.01         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        4.83         9.30         6.71         2.20         4.01        15.19 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.08         0.85        52.67        15.91         1.12         2.66 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QF 
        6.41         2.04         5.62        10.65         4.41         7.63 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A4AB TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A9SW 
        2.50         6.35        13.48         0.85         6.58        11.90 
TCGA-XF-A9SZ TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAN5 
       28.24        54.90         6.77        75.39 

$subtype3
TCGA-2F-A9KR TCGA-BT-A20P TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
      103.50        17.88         2.04         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA 
        0.07         0.10        12.92        16.31        66.41        19.00 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 
       15.62        10.59         9.67        41.56        76.60        24.66 
TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43X 
        0.10         0.66         0.82        45.93        14.93         3.62 
TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC 
       50.66         4.11         7.13         3.48         3.25        22.32 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GD-A3OQ 
        7.04        20.12        19.46         2.89         4.50         3.12 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3QK TCGA-K4-A54R TCGA-LT-A5Z6 
       11.31        27.09         6.41         6.67        10.52         3.45 
TCGA-LT-A8JT TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       11.80        45.04        15.35         1.87        17.88        64.80 
TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAN0 TCGA-YC-A8S6 
       23.64        16.27         2.10         7.63        56.48         4.83 
TCGA-YF-AA3L 
        7.96 

$subtype4
TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20X TCGA-BT-A3PH TCGA-C4-A0EZ 
       98.33         6.74        32.84         8.25         4.67         8.98 
TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3X1 
       23.01         0.10         9.34        18.41        50.27        48.00 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       41.06        30.67        26.17         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3SM TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR 
        0.56        12.99         6.12        22.98        12.13        13.38 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S TCGA-G2-A2EL TCGA-GC-A3RD TCGA-GD-A6C6 
        5.36        27.45         6.38        26.93        14.07         2.20 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA 
        6.15         5.69         7.79         4.14         6.41        11.54 
TCGA-K4-A6MB TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-AAN1 
        4.27         3.75        88.93        56.19        26.27        30.94 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3M 
       10.36         0.66         9.04 

$subtype5
TCGA-BT-A20R TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AD 
        5.06         5.59         0.46         4.90         2.53       112.44 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IU 
       17.62         1.81       123.85         3.98        10.49        20.02 
TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
      140.81        12.89        15.68        12.43        24.30        22.45 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62P TCGA-FD-A6TB 
       13.18        19.79        14.96         6.87         6.28        18.81 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EK TCGA-GC-A3OO 
        2.07         2.66        10.85         6.48         5.69        15.81 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A767 TCGA-K4-A83P 
       17.75         7.73         2.10         7.36         4.73         6.38 
TCGA-R3-A69X TCGA-XF-A9SI TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR 
       14.24        79.66         2.24        92.98        10.82        91.73 
TCGA-XF-AAN4 
       27.06 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.43     0.13     0.07     0.10     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
   97.45   130.88   103.50    98.33   140.81 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.045    6.755   10.520    9.340   10.850 
[1] "0.4 - 97.5 (12.0)"  "0.1 - 130.9 (6.8)"  "0.1 - 103.5 (10.5)"
[4] "0.1 - 98.3 (9.3)"   "0.5 - 140.8 (10.8)"
D8V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       14        24       19
  subtype2        0       1       15        25       30
  subtype3        0       1       33        13       13
  subtype4        1       0       16        17       11
  subtype5        0       0        9        14       19
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE 0A         0        0        0        1        0
  STAGE I          0        1        1        0        0
  STAGE II        14       15       33       16        9
  STAGE III       24       25       13       17       14
  STAGE IV        19       30       13       11       19
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       13 35  7
  subtype2       18 36 14
  subtype3       30 16  7
  subtype4       12 22  5
  subtype5        9 27  6
D8V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       13       18       30       12        9
  T3             35       36       16       22       27
  T4              7       14        7        5        6
[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       N0 N1 N2 N3
  subtype1 37  9  7  2
  subtype2 39  9 18  3
  subtype3 40  4  8  1
  subtype4 27  3  6  1
  subtype5 24  2 17  0
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       37       39       40       27       24
  N1        9        9        4        3        2
  N2        7       18        8        6       17
  N3        2        3        1        1        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"
          vv
clus       M0 M1 MX
  subtype1 29  0 29
  subtype2 30  1 40
  subtype3 38  1 22
  subtype4 19  3 23
  subtype5 15  2 26
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       29       30       38       19       15
  M1        0        1        1        3        2
  MX       29       40       22       23       26
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 20 38
  subtype2 12 60
  subtype3 15 46
  subtype4 11 34
  subtype5 19 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   38
  subtype2   12   60
  subtype3   15   46
  subtype4   11   34
  subtype5   19   24
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       20       12       15       11       19
  MALE         38       60       46       34       24
[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, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         4    46
  subtype2     8                         3    56
  subtype3    13                         3    40
  subtype4     5                         2    32
  subtype5     2                         2    39
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        8       13        5        2
  BLACK OR AFRICAN AMERICAN        4        3        3        2        2
  WHITE                           46       56       40       32       39
[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"
D8V12, binary
          cls
clus        0  1
  subtype1  0 53
  subtype2  1 66
  subtype3  2 56
  subtype4  1 41
  subtype5  1 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   53
  subtype2    1   66
  subtype3    2   56
  subtype4    1   41
  subtype5    1   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        2        1        1
  NOT HISPANIC OR LATINO       53       66       56       41       41
[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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 45 22
  subtype2 17 13
  subtype3 64 19
  subtype4 49 34
subtype1 subtype2 subtype3 subtype4 
      67       30       83       83 
subtype1 subtype2 subtype3 subtype4 
      22       13       19       34 
$subtype1
TCGA-2F-A9KO TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A3PJ 
       22.29         7.33        19.04        12.16         5.06        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 
        2.07        15.42         9.99        28.41         1.94         2.93 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW 
        0.43        12.92         7.79        87.32         7.82         8.28 
TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B5 
       10.55        41.06        15.35         1.22         0.46         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A43P 
        6.87        11.93        15.88        45.93         5.52        14.93 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       12.13        37.15         6.87         5.69         6.84        49.68 
TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3RC 
        6.71        61.94        30.61        17.26         2.24        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A40E 
        1.12         2.66         7.59         2.04         5.62         6.41 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI 
        9.01         8.22         6.48         1.81         6.35        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T4 
       16.67        88.93        97.45        23.64        21.04        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       66.64         2.10         8.32        75.39        10.36         0.66 
TCGA-YF-AA3M 
        9.04 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX 
       11.97        84.00         4.83        40.08         2.66        11.93 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A6AV 
        8.35         3.65         7.20         1.84       130.88        64.18 
TCGA-DK-A6B2 TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A6TH 
       15.68         1.97        22.98         6.87         4.83         2.20 
TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G 
       15.19         6.41        10.65         4.41         7.63        19.07 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-S5-A6DX TCGA-XF-AAMX 
        1.51        38.60         3.45         2.50         0.85         6.77 

$subtype3
TCGA-2F-A9KR TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42C 
      103.50        32.84        17.88        17.16         4.67        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98        23.01         2.04         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10         0.07         0.10         0.10         5.19        16.31 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A3IS 
       66.41        18.41        19.00        16.14        15.62        50.27 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A2PC 
        9.67        17.98        41.56        76.60        67.36        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17        24.66         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A5BV 
        0.66         1.38        12.99        19.79         3.62         5.36 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.11         4.01         7.13         3.48         4.08         3.25 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
       26.93        20.12         0.85        52.67        19.46         2.89 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A763 
        4.50        14.07         3.12         2.20        11.31        27.09 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         5.69         7.79         4.14         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       11.54         6.74         3.06        10.52         3.45        11.80 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HI 
       13.48         3.75        45.04         6.58        56.19        17.88 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-AAML TCGA-XF-AAN1 TCGA-YF-AA3L 
       26.27        18.90         7.63        30.94         7.96 

$subtype4
TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       98.33         6.74         6.58        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A72E 
       14.96         8.25         5.59         0.46         4.90         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        2.53         2.14         8.91       112.44        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
       10.59       123.85         2.20         3.98         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-FD-A3B3 TCGA-FD-A3B4 
       21.30        20.02       140.81        48.00        12.89        15.68 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        12.43        24.30        22.45         6.12        12.82 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BT 
       13.18        46.78        14.96        14.93        13.38        11.01 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       27.45         2.66         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EC 
        9.30         2.07         2.66        10.85         6.48        22.32 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP 
        5.69        35.24        15.81        17.75         7.73         2.10 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A767 TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6MB 
       20.98         7.36         4.73         8.75         4.67         4.27 
TCGA-K4-A83P TCGA-R3-A69X TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
        6.38        14.24         1.87        64.80        79.66        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       28.24         2.24        92.98        10.82        54.90        91.73 
TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 
        2.96        56.48        27.06         3.88         4.83 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.85     0.07     0.46 
subtype1 subtype2 subtype3 subtype4 
   97.45   130.88   103.50   140.81 
subtype1 subtype2 subtype3 subtype4 
   9.040    7.035    7.960   10.850 
[1] "0.4 - 97.5 (9.0)"   "0.8 - 130.9 (7.0)"  "0.1 - 103.5 (8.0)" 
[4] "0.5 - 140.8 (10.8)"
D9V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       20        24       22
  subtype2        0       1        3        11       15
  subtype3        1       1       41        26       19
  subtype4        0       0       17        29       36
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE 0A         0        0        1        0
  STAGE I          0        1        1        0
  STAGE II        20        3       41       17
  STAGE III       24       11       26       29
  STAGE IV        22       15       19       36
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       19 35  8
  subtype2        6 16  9
  subtype3       39 29 10
  subtype4       15 53 12
D9V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       19        6       39       15
  T3             35       16       29       53
  T4              8        9       10       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       N0 N1 N2 N3
  subtype1 42 11  7  3
  subtype2 13  4 11  2
  subtype3 59  7  9  2
  subtype4 47  5 29  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       42       13       59       47
  N1       11        4        7        5
  N2        7       11        9       29
  N3        3        2        2        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       M0 M1 MX
  subtype1 24  1 42
  subtype2 12  0 19
  subtype3 55  3 30
  subtype4 35  3 45
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       24       12       55       35
  M1        1        0        3        3
  MX       42       19       30       45
[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"
D9V7, binary
          cls
clus        0  1
  subtype1 20 47
  subtype2  5 26
  subtype3 20 69
  subtype4 32 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   47
  subtype2    5   26
  subtype3   20   69
  subtype4   32   51
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20        5       20       32
  MALE         47       26       69       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"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         6    54
  subtype2     1                         1    27
  subtype3    20                         2    57
  subtype4     5                         4    70
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1       20        5
  BLACK OR AFRICAN AMERICAN        6        1        2        4
  WHITE                           54       27       57       70
[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"
D9V12, binary
          cls
clus        0  1
  subtype1  1 62
  subtype2  0 28
  subtype3  2 80
  subtype4  2 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   62
  subtype2    0   28
  subtype3    2   80
  subtype4    2   78
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        2        2
  NOT HISPANIC OR LATINO       62       28       80       78
[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"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 34 20
  subtype2 19 12
  subtype3 46 13
  subtype4 24 22
  subtype5 15  2
  subtype6 37 19
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      54       31       59       46       17       56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      20       12       13       22        2       19 
$subtype1
TCGA-2F-A9KO TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LB TCGA-CF-A1HR 
       22.29         6.58        19.50         5.06         5.59         0.46 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 
        4.90        16.31         2.53       112.44        17.62        10.59 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 
      123.85         3.98        21.30        20.02       140.81        12.89 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SR 
        4.01        12.43        24.30        22.45        13.18        19.79 
TCGA-FD-A43S TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK 
       14.96        37.15        11.01         2.07         2.66        10.85 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 
        6.48        22.32         5.69        15.81        17.75         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A767 TCGA-K4-A3WS TCGA-K4-A83P 
        2.10        20.98         7.36         4.73         8.75         6.38 
TCGA-R3-A69X TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9T3 
       14.24         1.87        64.80        79.66        11.90         2.24 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 
       92.98        10.82        91.73        27.06         3.88         4.83 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX 
       11.97        84.00         4.83        40.08         2.66        11.93 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A5W6 
        8.35         3.65         2.93         0.13         7.20         1.84 
TCGA-DK-A1AC TCGA-DK-A3IK TCGA-DK-A6AV TCGA-E7-A677 TCGA-FD-A3SS TCGA-FD-A5C1 
      130.88         2.20        64.18         1.38         1.97        49.68 
TCGA-FD-A62O TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV 
        4.83         2.20        15.19         6.41        10.65         4.41 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB 
        7.63        19.07         1.51        38.60         3.45         2.50 
TCGA-XF-AAMX 
        6.77 

$subtype3
TCGA-2F-A9KR TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A47X 
      103.50         4.67        28.70         8.98         2.04         0.10 
TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 
        5.19        66.41        18.41        50.27         9.67        17.98 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       41.56        67.36        41.06        43.59        15.35        26.17 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A43N 
        0.49         0.53         0.59         0.56        12.99        22.98 
TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       14.93         5.36         4.11         7.13         3.48         4.08 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD 
       20.12         0.85        52.67        19.46         4.50        14.07 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.20        11.31         6.41         6.15         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A54R 
        4.14         6.67        11.54         6.74         3.06        10.52 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF 
        3.45        13.48        45.04         6.58        88.93        56.19 
TCGA-XF-A9T0 TCGA-XF-AAML TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       26.27         7.63        10.36         0.66         7.96 

$subtype4
TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20T 
       98.33         6.74        19.04        32.84        17.88        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F6 TCGA-CU-A72E TCGA-DK-A1A5 
       14.96         5.06         8.25        23.01         9.34         2.14 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3X1 TCGA-DK-A6B2 
        8.91        16.14         1.81        10.49        48.00        15.68 
TCGA-FD-A3B4 TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU 
       15.68         6.12        46.78        12.13        13.38         6.87 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.84        27.45         6.87         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GU-A42Q 
       18.81         9.30         4.01        26.93        35.24         7.59 
TCGA-GU-A766 TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A6MB TCGA-S5-A6DX TCGA-XF-A9SZ 
        5.62         9.01         4.67         4.27         0.85        28.24 
TCGA-XF-A9T2 TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-YF-AA3M 
       18.90        54.90         2.96         9.04 

$subtype5
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-DK-A1AA 
        0.69         0.07         0.10         0.07         0.10        19.00 
TCGA-DK-A1AG TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A5KF TCGA-FD-A43X TCGA-GC-A3BM 
       15.62        76.60        24.66         0.66         3.62         2.89 
TCGA-GU-A763 TCGA-LT-A8JT TCGA-S5-AA26 TCGA-XF-A8HI TCGA-XF-AAN1 
       27.09        11.80         3.75        17.88        30.94 

$subtype6
TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        7.33        12.16        17.16        12.82         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A2I2 
        9.99        28.41         1.94         0.43        12.92         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3WW TCGA-DK-A3WX TCGA-E7-A7DV 
       87.32         7.82         8.22         8.28        10.55         1.22 
TCGA-E7-A7XN TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        0.46         8.94         6.87        11.93        15.88        45.93 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43U TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TD 
       12.82         5.52        14.93         5.69         2.66         6.71 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3RC 
        3.25        61.94        30.61        17.26         2.24        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A762 TCGA-GV-A40E TCGA-HQ-A5NE 
        1.12         2.66         3.12         2.04         6.41         8.22 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.48         1.81         6.35        12.23        16.67        97.45 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMW 
       23.64        21.04        16.27        66.64         2.10         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN5 
       56.48        75.39 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.46     0.13     0.10     0.85     0.07     0.43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  140.81   130.88   103.50    98.33    76.60    97.45 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  12.165    6.410    8.980    9.915    3.750    8.630 
[1] "0.5 - 140.8 (12.2)" "0.1 - 130.9 (6.4)"  "0.1 - 103.5 (9.0)" 
[4] "0.8 - 98.3 (9.9)"   "0.1 - 76.6 (3.8)"   "0.4 - 97.5 (8.6)"  
D10V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       12        19       22
  subtype2        0       1        5        12       13
  subtype3        1       1       27        15       18
  subtype4        0       0       10        18       18
  subtype5        0       0       13         5        1
  subtype6        0       0       14        21       20
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE 0A         0        0        1        0        0        0
  STAGE I          0        1        1        0        0        0
  STAGE II        12        5       27       10       13       14
  STAGE III       19       12       15       18        5       21
  STAGE IV        22       13       18       18        1       20
[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"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       10 34  7
  subtype2        8 16  8
  subtype3       24 21  5
  subtype4        9 28  8
  subtype5       14  4  2
  subtype6       14 30  9
D10V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T0+T1+T2       10        8       24        9       14       14
  T3             34       16       21       28        4       30
  T4              7        8        5        8        2        9
[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       N0 N1 N2 N3
  subtype1 31  3 19  0
  subtype2 16  3 10  2
  subtype3 34  5  9  2
  subtype4 27  6 11  0
  subtype5 17  0  1  0
  subtype6 36 10  6  3
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       31       16       34       27       17       36
  N1        3        3        5        6        0       10
  N2       19       10        9       11        1        6
  N3        0        2        2        0        0        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       M0 M1 MX
  subtype1 21  2 31
  subtype2 15  0 17
  subtype3 31  4 26
  subtype4 21  1 24
  subtype5 17  0  3
  subtype6 21  0 35
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       21       15       31       21       17       21
  M1        2        0        4        1        0        0
  MX       31       17       26       24        3       35
[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"
D10V7, binary
          cls
clus        0  1
  subtype1 22 32
  subtype2  6 26
  subtype3 14 48
  subtype4 15 31
  subtype5  4 16
  subtype6 16 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   32
  subtype2    6   26
  subtype3   14   48
  subtype4   15   31
  subtype5    4   16
  subtype6   16   40
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       22        6       14       15        4       16
  MALE         32       26       48       31       16       40
[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"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    48
  subtype2     3                         1    25
  subtype3    10                         2    43
  subtype4     1                         4    34
  subtype5     8                         1    10
  subtype6     3                         3    48
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        3       10        1        8
  BLACK OR AFRICAN AMERICAN        2        1        2        4        1
  WHITE                           48       25       43       34       10
                           clus
vv                          subtype6
  ASIAN                            3
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           48
[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"
D10V12, binary
          cls
clus        0  1
  subtype1  1 51
  subtype2  0 28
  subtype3  2 55
  subtype4  1 41
  subtype5  0 20
  subtype6  1 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   51
  subtype2    0   28
  subtype3    2   55
  subtype4    1   41
  subtype5    0   20
  subtype6    1   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        2        1        0        1
  NOT HISPANIC OR LATINO       51       28       55       41       20       53
[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"
