[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/10005789/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/10668130/BLCA-TP.mergedcluster.txt"

nPatients in clinical file=218, in cluster file=367, common to both=218
[1]  10 218
[1] "CN_CNMF"
[1] 3
 1  2  3 
54 77 83 
 1  2  3 
54 77 83 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
77 48 49 40 
 1  2  3  4 
77 48 49 40 
[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 
91 60 65 
 1  2  3 
91 60 65 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
71 38 55 52 
 1  2  3  4 
71 38 55 52 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
57 93 66 
 1  2  3 
57 93 66 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
39 23 26 26 36 29 37 
 1  2  3  4  5  6  7 
39 23 26 26 36 29 37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
42 90 84 
 1  2  3 
42 90 84 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 39 111  66 
  1   2   3 
 39 111  66 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "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 218 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
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-CU-A0YN TCGA-CU-A0YO 
           3            2            3            3           NA           NA 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
         219          166          158          496           NA          284 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
          77           NA          955          560          578          271 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        3981         3420          491          536          475           55 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
         322           NA         3767         2656           67          121 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
         238           NA          319         1529          648          609 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
          NA          252           NA         4283         1460           NA 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
        1952         1476         2330         2049          477          982 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
         933         1326           NA          796          750            3 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
          15           16           NA           18           17           20 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
          42           25           37          392          477           NA 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
         209           NA          378          363          483         1397 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
          NA          683          501          390           NA          401 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
          NA           NA           60          699          454          455 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
         454          110          369          407         1130           NA 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
         209           NA           NA          208           NA          209 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        1511           81          147           NA          194         1541 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
         283          204          125           81           67          122 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
         462          217          106          124           NA          197 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
         679         1884          931          173           NA         1072 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
         525          214           NA           26           88           68 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
         481          137          484          428          540           34 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
          81          235           64           95          638           67 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
         195          233          344          134          195          187 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
         173          232           NA          237          126          203 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
         195          580          351           46          205         1174 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
         266          105          142           76          197          320 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
          53           55          130          194          193          105 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
         410          372          507         2705         2964         1709 
TCGA-XF-A8HG TCGA-YC-A8S6 
          NA          147 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=148,	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=1,	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=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=15,	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=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=25,	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"                       
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 218 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, 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  61 102  33 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      63      102       33 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  61 102  33 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      63      102       33 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
133  22  39   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
133  22  39   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
133  22  39   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
133  22  39   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=49, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 40 14
  subtype2 56 19
  subtype3 55 24
subtype1 subtype2 subtype3 
      54       75       79 
subtype1 subtype2 subtype3 
      14       19       24 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD 
       40.08         2.66         5.06         8.35        17.16         3.65 
TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 
       12.82         8.98         0.43         5.19         2.53        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
      130.88       112.44        10.59        87.32         3.98         7.82 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       67.36        32.28        15.35        26.17         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BY 
        0.56         1.22        24.30        22.98        14.93         6.84 
TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-G2-A2EF TCGA-G2-A3IE 
        6.87         9.30         4.11         2.66        61.94        20.12 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX 
        0.85         4.50         7.73         6.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         4.14         6.41        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HG 
        6.74        38.60         4.27         3.45        13.48        15.35 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PK 
        7.33         6.58        12.16         5.06        14.96         2.07 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       28.41         1.94         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AE TCGA-DK-A1AF 
        0.10        12.92         4.90         7.20        16.14        17.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        1.81         7.79       123.85         8.22        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
        9.67         8.28       140.81        48.53        76.60        15.68 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
        0.10         0.53         0.82        12.89        15.68         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SO 
        4.01        12.43        11.93        15.88        22.45         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       13.18        14.96        12.13        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 
        5.69         2.66         6.28         6.71         2.20        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-GC-A3OO 
        7.13         4.08        30.61         5.69        26.93        15.81 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-H4-A2HO 
       15.91        17.75         1.12         2.66         2.10         1.51 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        8.75         6.48        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.35        16.67        97.45 

$subtype3
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
        6.74        12.39        11.93        19.04        32.84        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       19.50        14.89         8.25         5.59         4.67        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47X 
       28.70         9.99        23.01         0.46         0.69         0.10 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46        16.31         1.84         9.34         2.14        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS 
       19.00         8.91        15.62         2.20        10.49        50.27 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A2PC 
       10.55        48.00        17.98        64.18        30.67        43.59 
TCGA-E7-A3X6 TCGA-E7-A5KF TCGA-E7-A677 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SM 
       24.66         0.66         1.38         8.94        45.93        16.47 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A43X 
       12.82        46.78        19.79         1.97        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S 
       13.38         5.36        27.45        49.68         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO 
       50.66         4.01         3.48         3.25         6.48        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A3OQ 
       17.26         7.04         2.89         2.24        14.07         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QK 
       20.98         2.20         7.66        11.31         4.41         6.67 
TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-PQ-A6FI TCGA-XF-A8HD 
       11.54         3.45         4.67         2.50        12.23        88.93 
TCGA-XF-A8HF 
       56.19 

subtype1 subtype2 subtype3 
    0.43     0.07     0.10 
subtype1 subtype2 subtype3 
  130.88   140.81    88.93 
subtype1 subtype2 subtype3 
    7.68     7.79    11.31 
[1] "0.4 - 130.9 (7.7)" "0.1 - 140.8 (7.8)" "0.1 - 88.9 (11.3)"
D1V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       1       16        12       23
  subtype2        0       1       29        29       18
  subtype3        1       0       23        31       26
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        0        1
  STAGE I          1        1        0
  STAGE II        16       29       23
  STAGE III       12       29       31
  STAGE IV        23       18       26
[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 25  7
  subtype2       26 34 11
  subtype3       21 42 14
D1V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       15       26       21
  T3             25       34       42
  T4              7       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 21  6 15  3
  subtype2 57  7  9  2
  subtype3 52  9 14  2
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       21       57       52
  N1        6        7        9
  N2       15        9       14
  N3        3        2        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 26  2 25
  subtype2 36  1 40
  subtype3 44  2 37
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       26       36       44
  M1        2        1        2
  MX       25       40       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"
D1V7, binary
          cls
clus        0  1
  subtype1 12 42
  subtype2 19 58
  subtype3 19 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   42
  subtype2   19   58
  subtype3   19   64
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       19       19
  MALE         42       58       64
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         3    43
  subtype2     8                         5    62
  subtype3    10                         3    65
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        8       10
  BLACK OR AFRICAN AMERICAN        3        5        3
  WHITE                           43       62       65
[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"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 53 23
  subtype2 35 13
  subtype3 34 12
  subtype4 28 10
subtype1 subtype2 subtype3 subtype4 
      76       48       46       38 
subtype1 subtype2 subtype3 subtype4 
      23       13       12       10 
$subtype1
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33        12.39         6.58        11.93        19.04        12.16 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
       14.96         5.06         8.25        17.16         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS 
        2.07         9.99        28.41         1.94         2.93         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I4 
       12.92         5.46         9.34        17.62         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW 
       87.32         7.82         8.22        10.49        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A7DV TCGA-FD-A3B3 
       10.55       140.81        32.28        43.59         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SM 
       15.68         8.94         6.87         4.01        12.43        16.47 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS 
        5.52        13.18        14.96        14.93        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
       11.01         6.87         5.69        49.68         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        6.38         9.30         6.71         6.48        61.94        30.61 
TCGA-G2-A2EL TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E 
       26.93        17.75         2.66        20.98         7.66         6.41 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         2.50         6.48         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35        12.23        16.67 

$subtype2
TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LB TCGA-C4-A0EZ TCGA-C4-A0F6 
       40.08         5.06         8.35         5.59         8.98        23.01 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK 
        2.53        18.41       130.88       112.44        10.59         2.20 
TCGA-DK-A3IL TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A4TZ 
        3.98        48.00        64.18        67.36        15.68        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR 
       26.17         0.49         0.56        45.93        24.30        19.79 
TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       22.98        13.38        27.45        15.19         7.13         4.08 
TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A2C5 
        5.69        20.12         0.85         4.50        14.07         7.73 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA 
        2.20         6.41         5.69         7.63         7.79        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.51         6.74        38.60         4.27         3.45        13.48 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A27C 
        6.74        32.84         4.67        15.42        28.70         0.69 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        0.07         0.10         5.19         2.14        31.40        19.00 
TCGA-DK-A1AE TCGA-DK-A3IS TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-E7-A3X6 TCGA-E7-A4XJ 
       16.14        50.27        17.98        48.53        24.66         0.53 
TCGA-E7-A541 TCGA-E7-A677 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SS 
        0.59         1.38        11.93        15.88        12.82         1.97 
TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TH 
        3.62         5.36         6.84         4.83         4.11         2.20 
TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM 
        4.01         3.25        35.24        17.26         7.04         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GV-A3JV TCGA-GV-A3JX 
        2.24        15.91         1.12         3.12         4.41         6.15 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A54R 
        4.14         6.67        19.07        10.52 

$subtype4
TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F7 TCGA-CF-A1HR 
        2.66        17.88        19.50        14.89         2.04         0.46 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.13         0.10         0.07         0.10         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IT 
       16.31         1.84         8.91        15.62         1.81        21.30 
TCGA-DK-A3IV TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A678 
        9.67        76.60        30.67         0.10         0.66         0.82 
TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TG 
       22.45        46.78        14.93         6.87        50.66         2.66 
TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-GC-A3OO TCGA-GD-A3OP TCGA-GU-A42R TCGA-GV-A3JW 
        3.48        22.32        15.81         2.10        11.31         6.41 
TCGA-K4-A3WS TCGA-YC-A8S6 
        8.75         4.83 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.49     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  140.81   130.88    50.27    76.60 
subtype1 subtype2 subtype3 subtype4 
   9.320    9.785    5.755    7.035 
[1] "0.4 - 140.8 (9.3)" "0.5 - 130.9 (9.8)" "0.1 - 50.3 (5.8)" 
[4] "0.1 - 76.6 (7.0)" 
D2V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       0       18        38       20
  subtype2        1       2       14        11       19
  subtype3        0       0       21        13       14
  subtype4        0       0       17         7       15
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE 0A         0        1        0        0
  STAGE I          0        2        0        0
  STAGE II        18       14       21       17
  STAGE III       38       11       13        7
  STAGE IV        20       19       14       15
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       16 40 16
  subtype2       14 22  5
  subtype3       20 22  5
  subtype4       13 14  7
D2V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       16       14       20       13
  T3             40       22       22       14
  T4             16        5        5        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 54  8  9  4
  subtype2 22  6 12  1
  subtype3 33  7  6  1
  subtype4 20  1 12  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       54       22       33       20
  N1        8        6        7        1
  N2        9       12        6       12
  N3        4        1        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 31  1 45
  subtype2 26  2 19
  subtype3 25  0 24
  subtype4 26  2 12
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       31       26       25       26
  M1        1        2        0        2
  MX       45       19       24       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"
D2V7, binary
          cls
clus        0  1
  subtype1 26 51
  subtype2 14 34
  subtype3  6 43
  subtype4  5 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   51
  subtype2   14   34
  subtype3    6   43
  subtype4    5   35
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       26       14        6        5
  MALE         51       34       43       35
[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"
D2V8, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         6    64
  subtype2     4                         1    39
  subtype3     8                         3    37
  subtype4     8                         2    27
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        4        8        8
  BLACK OR AFRICAN AMERICAN        6        1        3        2
  WHITE                           64       39       37       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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 27  6
  subtype2 17 11
  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       11       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        16.47         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        31.40        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     7.84    12.49     5.69    10.11 
[1] "0.1 - 130.9 (7.8)"  "1.8 - 140.8 (7.8)"  "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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 29 10
  subtype2 23 14
  subtype3 12 15
  subtype4 11  8
subtype1 subtype2 subtype3 subtype4 
      39       37       27       19 
subtype1 subtype2 subtype3 subtype4 
      10       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        31.40        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        16.47         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 
   10.59     8.35    14.89     8.28 
[1] "0.1 - 112.4 (10.6)" "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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 69 17
  subtype2 38 21
  subtype3 44 21
subtype1 subtype2 subtype3 
      86       59       65 
subtype1 subtype2 subtype3 
      17       21       21 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F6 
       40.08        17.88         8.35         4.67        28.70        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10         0.10         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG 
        1.84        31.40        18.41        19.00       112.44        15.62 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
        2.20         3.98        50.27         9.67        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3Y1 
       48.53        76.60        67.36        30.67        26.17         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3NA TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O 
        0.82        45.93        22.98         3.62         5.36         4.83 
TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       50.66         4.11         4.01        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY 
        4.08         3.25        22.32         5.69        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        2.89         4.50        14.07         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41        11.31         4.41         6.41         6.15         5.69 
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-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.51         6.74        38.60         4.27         3.45        13.48 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$subtype2
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        19.04        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-C4-A0EZ 
       19.50         5.06        17.16         5.59         3.65         8.98 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
        2.53         2.14       130.88        17.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY 
      123.85         8.22        10.49        21.30        20.02       140.81 
TCGA-DK-A6B2 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.68         1.22         4.01        12.43        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       16.47        12.82        13.18        46.78        19.79        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       14.96        14.93        13.38        37.15        11.01         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
       27.45         6.87         2.66         6.28         6.38         9.30 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2EO TCGA-GC-A3OO TCGA-K4-A3WS 
        2.66         2.20         6.48        35.24        15.81         8.75 
TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-XF-A8HD 
        3.45        10.52         1.74         6.38        88.93 

$subtype3
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
        6.58        11.93        32.84        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        12.82         2.07         9.99        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E 
        2.93         2.04         0.43        12.92         5.46         9.34 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW 
        8.91        16.14         7.79        87.32         7.82         8.28 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       10.55        17.98        32.28        43.59        15.35        24.66 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89        15.68         8.94         6.87        11.93        15.88 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 
        5.52         1.97        12.13         6.87         6.84        49.68 
TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
        6.71        61.94        30.61        26.93        17.26         7.04 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
        2.24        15.91        17.75         1.12         2.66         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       20.98         7.66         6.41         4.67         2.50         6.48 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        1.81         6.35        12.23        16.67        97.45 

subtype1 subtype2 subtype3 
    0.07     1.22     0.43 
subtype1 subtype2 subtype3 
  112.44   140.81    97.45 
subtype1 subtype2 subtype3 
    6.28    11.01     9.34 
[1] "0.1 - 112.4 (6.3)"  "1.2 - 140.8 (11.0)" "0.4 - 97.5 (9.3)"  
D5V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        1       2       39        23       23
  subtype2        0       0       11        24       25
  subtype3        0       0       19        26       19
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         1        0        0
  STAGE I          2        0        0
  STAGE II        39       11       19
  STAGE III       23       24       26
  STAGE IV        23       25       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       35 33  9
  subtype2       12 38 10
  subtype3       15 30 14
D5V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       35       12       15
  T3             33       38       30
  T4              9       10       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 55  6 16  2
  subtype2 36  7 15  2
  subtype3 41  8  8  3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       55       36       41
  N1        6        7        8
  N2       16       15        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 55  2 33
  subtype2 23  3 34
  subtype3 31  0 34
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       55       23       31
  M1        2        3        0
  MX       33       34       34
[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 16 75
  subtype2 14 46
  subtype3 21 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   75
  subtype2   14   46
  subtype3   21   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       16       14       21
  MALE         75       46       44
[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    20                         2    65
  subtype2     1                         3    52
  subtype3     1                         7    52
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           20        1        1
  BLACK OR AFRICAN AMERICAN        2        3        7
  WHITE                           65       52       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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 55 11
  subtype2 19 18
  subtype3 37 18
  subtype4 40 12
subtype1 subtype2 subtype3 subtype4 
      66       37       55       52 
subtype1 subtype2 subtype3 subtype4 
      11       18       18       12 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A47S 
       40.08        17.88         8.35        28.70         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3QU 
        0.07         0.10         0.07         0.10         0.10         5.19 
TCGA-CU-A3YL TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AG TCGA-DK-A3IK 
       16.31        18.41        19.00       130.88        15.62         2.20 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       50.27         9.67        64.18        48.53        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-FD-A43P TCGA-FD-A43X 
        0.56         0.66         1.38         0.82        14.93         3.62 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        5.36         4.83         4.11        15.19         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-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41        11.31         4.41         6.41         6.15         5.69 
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-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HG 
        1.51         6.74        38.60         3.45        13.48        15.35 

$subtype2
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-DK-A3X2 TCGA-E5-A4TZ 
       87.32         8.22        20.02       140.81        17.98        15.35 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SP TCGA-FD-A3SS 
        1.22         6.87         4.01        12.43        13.18         1.97 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TH 
       37.15        11.01         5.69         2.66         6.38         2.20 
TCGA-FT-A61P TCGA-G2-A2EL TCGA-GD-A3OS TCGA-GV-A40E TCGA-K4-A3WV TCGA-K4-A5RJ 
        6.48        26.93        20.98         6.41         4.67         1.74 
TCGA-XF-A8HD 
       88.93 

$subtype3
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A2LB 
        2.66        32.84        19.50         5.06        14.89         5.59 
TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 
        4.67        23.01         0.46         4.90         7.20         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        2.53         2.14        31.40       112.44        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B2 
       10.59         3.98        10.49        21.30        48.00        15.68 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       45.93        24.30        22.45        16.47        12.82        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ 
       19.79        22.98        14.96        14.93        13.38        27.45 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
        6.87         6.28        50.66         9.30         2.66         4.01 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A2C5 
       22.32         5.69        35.24        15.81        14.07         7.73 
TCGA-GD-A3OP TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P 
        2.10         8.75         3.45        10.52         4.27         6.38 
TCGA-XF-A8HF 
       56.19 

$subtype4
TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
       11.93        14.96         8.25        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ 
       28.41         1.94         2.93         0.43        12.92         5.46 
TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW 
        9.34         8.91        16.14         7.79         7.82         8.28 
TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B3 TCGA-FD-A3B4 
       10.55        32.28        43.59        24.66        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU 
        8.94        11.93        15.88         5.52        12.13         6.87 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        6.84        49.68         6.71         3.25        61.94        30.61 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       17.26         7.04         2.24        15.91        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ 
        2.66         3.12         7.66         2.50         6.48         1.81 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.35        12.23        16.67        97.45 

subtype1 subtype2 subtype3 subtype4 
    0.07     1.22     0.46     0.43 
subtype1 subtype2 subtype3 subtype4 
  130.88   140.81   112.44    97.45 
subtype1 subtype2 subtype3 subtype4 
    6.28     8.22    12.82     9.14 
[1] "0.1 - 130.9 (6.3)"  "1.2 - 140.8 (8.2)"  "0.5 - 112.4 (12.8)"
[4] "0.4 - 97.5 (9.1)"  
D6V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        1       2       37        17       12
  subtype2        0       0        9        16       13
  subtype3        0       0        9        15       30
  subtype4        0       0       14        25       12
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE 0A         1        0        0        0
  STAGE I          2        0        0        0
  STAGE II        37        9        9       14
  STAGE III       17       16       15       25
  STAGE IV        12       13       30       12
[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       33 21  5
  subtype2        7 20  8
  subtype3       10 33 10
  subtype4       12 27 10
D6V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       33        7       10       12
  T3             21       20       33       27
  T4              5        8       10       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 46  3  8  2
  subtype2 23  4  6  3
  subtype3 26  8 21  0
  subtype4 37  6  4  2
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       46       23       26       37
  N1        3        4        8        6
  N2        8        6       21        4
  N3        2        3        0        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 44  2 24
  subtype2 13  1 24
  subtype3 27  2 26
  subtype4 25  0 27
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       44       13       27       25
  M1        2        1        2        0
  MX       24       24       26       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  8 63
  subtype2  9 29
  subtype3 15 40
  subtype4 19 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   63
  subtype2    9   29
  subtype3   15   40
  subtype4   19   33
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8        9       15       19
  MALE         63       29       40       33
[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    19                         2    48
  subtype2     1                         3    31
  subtype3     1                         1    47
  subtype4     1                         6    43
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                           19        1        1        1
  BLACK OR AFRICAN AMERICAN        2        3        1        6
  WHITE                           48       31       47       43
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 40 14
  subtype2 69 21
  subtype3 42 24
subtype1 subtype2 subtype3 
      54       90       66 
subtype1 subtype2 subtype3 
      14       21       24 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD 
       40.08         7.33         2.66        11.93         8.35         3.65 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU 
        2.07        28.70         2.93         0.13         7.20         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.84         2.14       130.88        10.59        87.32         2.20 
TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 TCGA-E7-A7DV 
       21.30        64.18        67.36        15.68         1.38         1.22 
TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5C0 
        4.01        12.82         5.52         1.97        22.98         6.87 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       49.68         4.83        50.66         9.30         6.71         4.11 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS 
        2.20         4.01        15.19         4.08         0.85         1.12 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.41         4.41         7.63        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V 
       38.60         3.45         2.50         4.27         6.35        13.48 

$subtype2
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
        6.74        32.84        17.88         4.67        12.82        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C 
        9.99        28.41         8.98        23.01         2.04         0.69 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG 
        5.46        16.31        31.40        18.41        19.00        15.62 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 
        7.82        50.27         9.67         8.28        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       17.98        48.53        76.60        32.28        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.59         0.56         0.66         0.82         8.94         6.87 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BV 
       15.88        45.93        14.93        14.93         3.62         5.36 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        7.13         3.48         3.25        61.94        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26         7.04        20.12         2.89         2.24 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 
        4.50        15.91        14.07         2.66         3.12         2.20 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       11.31         6.41         6.15         5.69         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        6.67         6.41        11.54        10.52         1.74         1.81 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        12.23        88.93        97.45        56.19        15.35 

$subtype3
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
        6.58        19.04        12.16        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-C4-A0F0 
       14.96         5.06         8.25        17.16         5.59         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AB 
        0.46         0.43         4.90         9.34         2.53         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        16.14        17.62         1.81         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 
        3.98         8.22        10.49        20.02       140.81        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       15.68        12.43        11.93        24.30        22.45        16.47 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR 
       13.18        46.78        19.79        14.96        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       37.15        11.01         6.87         5.69         6.84        27.45 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EC 
        2.66         6.28         6.38         2.66         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-GU-A42Q TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A83P TCGA-PQ-A6FN 
        7.66         8.75         4.67         6.48         6.38        16.67 

subtype1 subtype2 subtype3 
    0.13     0.07     0.43 
subtype1 subtype2 subtype3 
  130.88    97.45   140.81 
subtype1 subtype2 subtype3 
    6.38     9.83    10.75 
[1] "0.1 - 130.9 (6.4)"  "0.1 - 97.5 (9.8)"   "0.4 - 140.8 (10.8)"
D7V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       1       12        18       25
  subtype2        1       1       43        30       17
  subtype3        0       0       14        24       26
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        1        0
  STAGE I          1        1        0
  STAGE II        12       43       14
  STAGE III       18       30       24
  STAGE IV        25       17       26
[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 27 11
  subtype2       35 35 10
  subtype3       12 40 11
D7V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       15       35       12
  T3             27       35       40
  T4             11       10       11
[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 29 10 12  3
  subtype2 63  7  8  3
  subtype3 39  5 19  1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       29       63       39
  N1       10        7        5
  N2       12        8       19
  N3        3        3        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 27  1 28
  subtype2 53  2 38
  subtype3 29  2 35
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       27       53       29
  M1        1        2        2
  MX       28       38       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"
D7V7, binary
          cls
clus        0  1
  subtype1  8 49
  subtype2 17 76
  subtype3 25 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   49
  subtype2   17   76
  subtype3   25   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       17       25
  MALE         49       76       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"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         2    44
  subtype2    13                         4    71
  subtype3     3                         6    54
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6       13        3
  BLACK OR AFRICAN AMERICAN        2        4        6
  WHITE                           44       71       54
[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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 26 10
  subtype2 16  7
  subtype3 19  7
  subtype4 13 13
  subtype5 26 10
  subtype6 22  7
  subtype7 29  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      36       23       26       26       36       29       34 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      10        7        7       13       10        7        5 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       40.08         2.66        11.93         8.35         3.65        28.70 
TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IK 
        2.93         0.13         5.19         1.84       130.88         2.20 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 TCGA-FD-A3SS TCGA-FD-A5BZ 
       64.18        67.36        15.68         1.38         1.97        27.45 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
        4.83        50.66         9.30         4.11         2.20        15.19 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G 
        4.08         0.85         6.41         4.41         7.63        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A6MB TCGA-MV-A51V 
        1.51         6.74        38.60         3.45         4.27        13.48 

$subtype2
TCGA-BL-A13I TCGA-BT-A3PK TCGA-BT-A42E TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A2I6 
        7.33         2.07         9.99         7.20         2.14        87.32 
TCGA-DK-A3IT TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ 
       21.30         1.22         4.01        12.82         5.52        46.78 
TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TI TCGA-GC-A3RC 
       11.01         6.87        49.68         6.71         4.01        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-K4-A3WS TCGA-K4-A4AB TCGA-LC-A66R 
        1.12         2.66         8.75         2.50         6.35 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A47X TCGA-DK-A1A7 
        6.74        32.84         4.67        23.01         0.10        18.41 
TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       48.00        30.67        26.17         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-FD-A43N TCGA-FD-A5BV TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A6C6 
        0.56        22.98         5.36         4.50        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-XF-A8HD TCGA-XF-A8HF 
       88.93        56.19 

$subtype4
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20U TCGA-BT-A20V 
        6.58        19.04        12.16        17.88        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CU-A72E TCGA-DK-A1AE 
        8.25        17.16         8.98         2.04         9.34        16.14 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-FD-A3SM 
        8.22        50.27        32.28        43.59        15.35        16.47 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A62S TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GD-A3OS 
       12.13        37.15         6.38        26.93        20.12        20.98 
TCGA-K4-A3WV TCGA-K4-A5RJ 
        4.67         1.74 

$subtype5
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CU-A0YO 
       19.50         5.06        14.89         5.59         0.46         4.90 
TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 
        2.53         8.91       112.44        17.62         1.81       123.85 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 
        3.98        10.49        20.02       140.81        12.89        15.68 
TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S 
       12.43        24.30        22.45        13.18        19.79        14.96 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TG TCGA-FT-A61P 
       13.38         6.87         6.84         6.28         2.66         6.48 
TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-K4-A83P 
        5.69        15.81        17.75         7.73         2.10         6.38 

$subtype6
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3KJ 
       12.82        15.42        28.41         1.94         0.43         5.46 
TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-FD-A3B5 
        7.79         7.82         8.28        10.55        17.98         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A5BX TCGA-FD-A62N 
        6.87        11.93        15.88        14.93         5.69         2.66 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GU-A42Q 
       61.94        30.61        35.24        17.26         2.24         7.66 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.48         1.81        12.23        16.67        97.45 

$subtype7
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.69         0.07         0.10         0.07         0.10        12.92 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IV 
       16.31        31.40        19.00        15.62        10.59         9.67 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A678 
       48.53        76.60        24.66         0.10         0.66         0.82 
TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43X TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
       45.93        14.93         3.62         7.13         3.48         3.25 
TCGA-G2-A2EC TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GV-A3JW 
       22.32         7.04         2.89         3.12        11.31         6.41 
TCGA-GV-A3QK TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-XF-A8HG 
        6.67        10.52         3.45        15.35 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.13     1.12     0.10     1.74     0.46     0.43     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  130.88    87.32    88.93    50.27   140.81    97.45    76.60 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   5.800    6.870    6.575   15.155   11.460   10.550    7.085 
[1] "0.1 - 130.9 (5.8)"  "1.1 - 87.3 (6.9)"   "0.1 - 88.9 (6.6)"  
[4] "1.7 - 50.3 (15.2)"  "0.5 - 140.8 (11.5)" "0.4 - 97.5 (10.6)" 
[7] "0.1 - 76.6 (7.1)"  
D8V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       1        9        11       17
  subtype2        0       0        4         9       10
  subtype3        1       0        9        13        3
  subtype4        0       0        7        10        9
  subtype5        0       0        7        10       18
  subtype6        0       0        9        12        7
  subtype7        0       1       24         7        4
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE 0A         0        0        1        0        0        0        0
  STAGE I          1        0        0        0        0        0        1
  STAGE II         9        4        9        7        7        9       24
  STAGE III       11        9       13       10       10       12        7
  STAGE IV        17       10        3        9       18        7        4
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       10 18  7
  subtype2        6 13  4
  subtype3        7 15  1
  subtype4        5 10  8
  subtype5        7 22  6
  subtype6        7 18  2
  subtype7       20  6  4
D8V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1+T2       10        6        7        5        7        7       20
  T3             18       13       15       10       22       18        6
  T4              7        4        1        8        6        2        4
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 18  7  9  2
  subtype2 14  4  4  1
  subtype3 19  0  2  1
  subtype4 15  2  7  0
  subtype5 18  3 14  0
  subtype6 21  4  2  2
  subtype7 26  2  1  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       18       14       19       15       18       21       26
  N1        7        4        0        2        3        4        2
  N2        9        4        2        7       14        2        1
  N3        2        1        1        0        0        2        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 21  1 16
  subtype2  7  0 16
  subtype3 12  0 14
  subtype4 12  2 12
  subtype5 17  1 18
  subtype6 15  0 14
  subtype7 25  1 11
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       21        7       12       12       17       15       25
  M1        1        0        0        2        1        0        1
  MX       16       16       14       12       18       14       11
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1  6 33
  subtype2  3 20
  subtype3  6 20
  subtype4  8 18
  subtype5 15 21
  subtype6  7 22
  subtype7  5 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   33
  subtype2    3   20
  subtype3    6   20
  subtype4    8   18
  subtype5   15   21
  subtype6    7   22
  subtype7    5   32
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        6        3        6        8       15        7        5
  MALE         33       20       20       18       21       22       32
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         1    27
  subtype2     0                         1    21
  subtype3     4                         0    19
  subtype4     0                         2    21
  subtype5     1                         2    33
  subtype6     2                         3    23
  subtype7     9                         3    25
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            6        0        4        0        1
  BLACK OR AFRICAN AMERICAN        1        1        0        2        2
  WHITE                           27       21       19       21       33
                           clus
vv                          subtype6 subtype7
  ASIAN                            2        9
  BLACK OR AFRICAN AMERICAN        3        3
  WHITE                           23       25
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 29 10
  subtype2 59 31
  subtype3 63 18
subtype1 subtype2 subtype3 
      39       90       81 
subtype1 subtype2 subtype3 
      10       31       18 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       40.08         2.66        11.93         8.35         3.65        28.70 
TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC 
        2.93         0.13         7.20         1.84         2.14       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-E7-A677 TCGA-FD-A3SS 
       87.32         2.20        64.18        15.68         1.38         1.97 
TCGA-FD-A43N TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC 
       22.98         6.87        49.68         4.83        50.66         9.30 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF 
        2.20         4.01        15.19         6.41         4.41         7.63 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07         1.51         6.74        38.60         3.45         2.50 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V 
        4.27         6.35        13.48 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
        7.33         6.58        19.04        12.16        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PJ 
       14.89        14.96         5.06         8.25         5.59        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
        2.07        15.42        28.41         1.94         0.46         0.43 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD 
        4.90         5.46         9.34         2.53         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        3.98         8.22        10.49        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       10.55       140.81         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87         4.01        12.43        11.93        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S 
       12.82         5.52        13.18        46.78        19.79        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        5.69         6.84        27.45         2.66         6.28         6.38 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK 
        6.71         2.66         6.48        22.32        61.94         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A3YS 
       35.24        17.26         2.24        15.81        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42Q TCGA-K4-A3WS 
        2.66         7.73         2.10        20.98         7.66         8.75 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A83P TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.48         1.74         6.38        12.23        16.67        97.45 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42E 
        6.74        32.84        17.88        17.16         4.67         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         2.04         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10        12.92         5.19        16.31 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IS 
       31.40        18.41        19.00        15.62         7.82        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        48.00        17.98        48.53        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       32.28        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A678 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43P TCGA-FD-A43X 
        0.82        15.88        45.93        16.47        14.93         3.62 
TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        5.36         4.11         7.13         3.48         4.08         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       30.61        26.93         7.04        20.12         0.85         2.89 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R 
        4.50        15.91        14.07         3.12         2.20        11.31 
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-A40E TCGA-GV-A6ZA TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A6FZ TCGA-LT-A5Z6 
        6.41        11.54         4.67        10.52         1.81         3.45 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        56.19        15.35 

subtype1 subtype2 subtype3 
    0.13     0.43     0.07 
subtype1 subtype2 subtype3 
  130.88   140.81    88.93 
subtype1 subtype2 subtype3 
   6.740    9.915    7.820 
[1] "0.1 - 130.9 (6.7)" "0.4 - 140.8 (9.9)" "0.1 - 88.9 (7.8)" 
D9V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       1        8        13       19
  subtype2        0       0       21        34       33
  subtype3        1       1       40        25       16
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        0        1
  STAGE I          1        0        1
  STAGE II         8       21       40
  STAGE III       13       34       25
  STAGE IV        19       33       16
[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 19 10
  subtype2       18 54 14
  subtype3       33 29  8
D9V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       11       18       33
  T3             19       54       29
  T4             10       14        8
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20  7 11  2
  subtype2 56 10 19  3
  subtype3 55  5  9  2
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       20       56       55
  N1        7       10        5
  N2       11       19        9
  N3        2        3        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 21  1 20
  subtype2 39  1 50
  subtype3 49  3 31
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       21       39       49
  M1        1        1        3
  MX       20       50       31
[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"
D9V7, binary
          cls
clus        0  1
  subtype1  6 36
  subtype2 28 62
  subtype3 16 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   36
  subtype2   28   62
  subtype3   16   68
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       28       16
  MALE         36       62       68
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         1    31
  subtype2     3                         8    77
  subtype3    14                         3    61
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5        3       14
  BLACK OR AFRICAN AMERICAN        1        8        3
  WHITE                           31       77       61
[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"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 26 10
  subtype2 78 33
  subtype3 47 16
subtype1 subtype2 subtype3 
      36      111       63 
subtype1 subtype2 subtype3 
      10       33       16 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       40.08         2.66        11.93         8.35         3.65        28.70 
TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A6AV 
        2.93         0.13         5.19         1.84       130.88        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 TCGA-FD-A3SS TCGA-FD-A5BZ TCGA-FD-A62O 
       67.36        15.68         1.38         1.97        27.45         4.83 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
       50.66         9.30         4.11        15.19         4.08         0.85 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.41         4.41         7.63        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-MV-A51V TCGA-XF-A8HF 
       38.60         3.45         2.50         4.27        13.48        56.19 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.58        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.89        14.96         8.25        17.16         5.59 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       12.82         2.07        15.42         9.99        28.41         1.94 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        2.04         0.46         0.43        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AB 
        5.46        16.31         9.34         2.53         2.14         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E7-A3X6 
       21.30        20.02         8.28        10.55       140.81        24.66 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        15.88        24.30        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U 
       12.82         5.52        13.18        46.78        14.96        14.93 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        6.84         6.87        49.68         2.66         6.28         6.38 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2EC 
        6.71         2.66         2.20         4.01         6.48        22.32 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        35.24        17.26         7.04 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        2.24        15.81        15.91        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E TCGA-K4-A3WS 
        7.73         2.10        20.98         7.66         6.41         8.75 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        4.67         6.48         1.74         1.81         6.38         6.35 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
       12.23        16.67        97.45 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 
        6.74        32.84         5.06         4.67         8.98        23.01 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.07         0.10         0.07         0.10         0.10 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IS 
       31.40        18.41        19.00        15.62       123.85        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
        9.67        48.00        17.98        48.53        76.60        32.28 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       30.67        43.59        15.35        26.17         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3NA 
        0.53         0.59         0.56         0.66         0.82        45.93 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BV TCGA-FJ-A3Z9 
       19.79        22.98        14.93         3.62         5.36         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3RB 
        3.48         3.25        26.93        20.12         2.89         4.50 
TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX 
       14.07         3.12         2.20        11.31         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A54R 
        5.69         7.79         4.14         6.67        11.54        10.52 
TCGA-LT-A5Z6 TCGA-XF-A8HD TCGA-XF-A8HG 
        3.45        88.93        15.35 

subtype1 subtype2 subtype3 
    0.13     0.43     0.07 
subtype1 subtype2 subtype3 
  130.88   140.81   123.85 
subtype1 subtype2 subtype3 
   6.575    8.940    7.790 
[1] "0.1 - 130.9 (6.6)" "0.4 - 140.8 (8.9)" "0.1 - 123.8 (7.8)"
D10V2, continuous
          vv
clus       STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  subtype1        0       1        9        13       15
  subtype2        0       0       29        41       39
  subtype3        1       1       31        18       14
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE 0A         0        0        1
  STAGE I          1        0        1
  STAGE II         9       29       31
  STAGE III       13       41       18
  STAGE IV        15       39       14
[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       10 17  8
  subtype2       25 63 16
  subtype3       27 22  8
D10V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       10       25       27
  T3             17       63       22
  T4              8       16        8
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20  7  7  2
  subtype2 68 11 24  3
  subtype3 43  4  8  2
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       20       68       43
  N1        7       11        4
  N2        7       24        8
  N3        2        3        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 21  1 16
  subtype2 51  2 58
  subtype3 37  2 27
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       21       51       37
  M1        1        2        2
  MX       16       58       27
[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"
D10V7, binary
          cls
clus        0  1
  subtype1  6 33
  subtype2 32 79
  subtype3 12 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   33
  subtype2   32   79
  subtype3   12   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       32       12
  MALE         33       79       54
[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"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         1    27
  subtype2     3                         9    95
  subtype3    13                         2    47
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        3       13
  BLACK OR AFRICAN AMERICAN        1        9        2
  WHITE                           27       95       47
[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"
