[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"        "-oTSTAD-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/STAD-TP/10006301/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/10667981/STAD-TP.mergedcluster.txt"

nPatients in clinical file=351, in cluster file=386, common to both=351
[1]  10 351
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
160  30  62  10  84 
  1   2   3   4   5 
160  30  62  10  84 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
113  88 102 
  1   2   3 
113  88 102 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
82 91 91 
 1  2  3 
82 91 91 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
34 84 55 91 
 1  2  3  4 
34 84 55 91 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
66 63 46 37 62 
 1  2  3  4  5 
66 63 46 37 62 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
38 21 50 62 42 40 21 
 1  2  3  4  5  6  7 
38 21 50 62 42 40 21 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
117 103 127 
  1   2   3 
117 103 127 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
169  81  97 
  1   2   3 
169  81  97 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 78 126  96 
  1   2   3 
 78 126  96 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
166  60  74 
  1   2   3 
166  60  74 
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 351 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171          356           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA         1055          485           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
         399          308          416          213         1190           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19          997          421          402          491           38 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
         273          642          940          949         1002          390 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
         280          753         1072          728          469          852 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          564          378           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
         388          569          532           25           40           21 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
         373           15          625           22            8          394 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
           8          496           47           45          225          188 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
         593           11           NA          675           90           29 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
         418          131          427          101           11          583 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
         450           21            8          482          113          164 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
          22          280          615           34          389          481 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
          65          409            6          229           15          351 
TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
          NA          481          500           18          477           19 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
         325          382           35           20           92           69 
TCGA-BR-A4CR TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
          NA           28          408          411          392           24 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
          NA          431           16          390           20          589 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
         411           14          628          621           35          415 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
         352          156           86           99          400          401 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
           9            2           NA           12            2            2 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
           2            2            3            4            5            3 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
           3            4           NA            4            3            2 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
           4            4            4            4            2            3 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
           3            3           NA           92          822          485 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
          NA          243          245         1645           NA           NA 
TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
          NA          912         1431          580          366           NA 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
          NA           NA          577           NA          365           NA 
TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
         699           NA          942           NA           NA           31 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
          31           NA          183           30         3196           NA 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
          NA           NA         2405         1980          122         1674 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
          NA           NA          376          385          363          582 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
         625          573          564          566          543          406 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
         523          312          463          486          389          321 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
         344          375          752          511          593          523 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
           7          212          643          636          434          500 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
         180          461          419          449          417          342 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
         344           NA          297           90          476           NA 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
         225           NA           19          237          494          200 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
         440           NA          647          247           12          594 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
          92          678          519           NA           NA          413 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-7131 TCGA-HF-7132 
          17          337           47            7           NA           NA 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
          NA           NA           NA          550           NA           46 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
          NA          434          383          431          347          368 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
         323           23          739          170          374          360 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
         736           99          692          785          358          650 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
         912          273           NA          198          190          310 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
           8           64          394          589          538          374 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
         294          270          268          834          645           NA 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
         572           NA          559          163          158          398 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
          NA          196          209          169           55           77 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
         169         1842           NA          137           NA           NA 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
          NA           NA         3720         1153         1236         3519 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
        3540         2171           NA           NA         1083           NA 
TCGA-SW-A7EB TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
         176          128           NA 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=212,	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=11,	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=7,	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:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=20,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 351 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 20  86 149  86 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20  86 149  86 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 20  86 149  86 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20  86 149  86 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
111  94  66  68 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
111  94  66  68 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
111  94  66  68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
111  94  66  68 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=8, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=29, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1 100  48
  subtype2  20   9
  subtype3  40  14
  subtype4   6   1
  subtype5  56  21
subtype1 subtype2 subtype3 subtype4 subtype5 
     148       29       54        7       77 
subtype1 subtype2 subtype3 subtype4 subtype5 
      48        9       14        1       21 
$subtype1
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 
        5.62         6.97         4.64         7.43        30.90         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.12        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       23.93         0.16        12.43         0.69        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       16.31         6.18         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
        0.26        15.85         3.72         1.12        12.79         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 
       13.45         0.20         7.53         0.49        15.81        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       12.56         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL 
       14.17         0.53        12.82        19.36         0.46        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8531 
        5.13         2.83        13.18         0.07         0.13         0.10 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
        0.10         0.10         0.10        15.95         1.02         8.05 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        9.01        30.97         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6522 
      105.07        65.10        21.07         7.99        12.36        18.61 
TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       17.85        24.72        16.80        17.19        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        9.76         4.34         7.13         6.58        14.47        21.27 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB 
        3.02        22.29        59.54         5.03         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        5.59        11.84        24.20        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-MX-A5UG 
        6.51        10.19         0.26         8.88         8.81         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.50        11.05         4.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
      116.38        71.38        57.44         4.21 

$subtype2
TCGA-B7-5818 TCGA-BR-6801 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8682 TCGA-BR-8690 
       11.70        21.11         0.36         5.39        16.44        10.68 
TCGA-BR-A44U TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4304 
        1.15        13.51        20.42         0.07        20.02        27.02 
TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-D7-5578 
        4.01         7.07         1.02        28.96        79.07        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8576 TCGA-FP-A4BF 
       19.13        18.54        15.98        19.50         6.97         1.55 
TCGA-HU-A4G6 TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-RD-A8N6 TCGA-SW-A7EB 
       12.30         6.87         5.56         8.94         5.79 

$subtype3
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-7959 TCGA-BR-8296 TCGA-BR-8297 
        6.61        18.35        10.13        18.71         1.48         7.40 
TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CS 
       19.50         0.72        15.81         0.59         0.62         0.92 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8524 
        0.72         0.66        20.65         1.15         3.25         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A487 
        0.07         0.07         0.16         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5724 
        0.13         3.02        12.03        12.00         1.02        12.03 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV 
       20.55        18.84        13.35         0.23        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-HU-8238 TCGA-HU-A4GU 
       11.31         7.40         8.12        17.06         1.51         6.25 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       17.69         9.67        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-RD-A7C1 TCGA-RD-A8MV 
        5.36         6.44         5.56         1.81        16.67       122.30 

$subtype4
TCGA-BR-8369 TCGA-CG-4441 TCGA-D7-6817 TCGA-HU-8244 TCGA-HU-A4GC TCGA-HU-A4GP 
       14.04        14.01        12.79        14.27         3.25         8.98 
TCGA-HU-A4H3 
       19.36 

$subtype5
TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.18         7.00         0.62         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
       28.01         0.69        18.54         0.95         1.32         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 
       12.95         0.26         1.55        14.79         9.21        20.22 
TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 
       11.54         0.66         2.27        13.64        13.15         0.30 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.07         0.10         0.13         0.07         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        0.10         7.99        54.08        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       21.99        18.97        22.98        15.02         4.01        55.04 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       11.93        17.19        10.26        15.22        10.55        11.31 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       12.33        14.27         2.96        15.65         0.62         7.79 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 
       16.24        72.23         0.39        19.53        13.58         0.56 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.92        12.59        14.17        22.75        25.81        11.77 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL 
        2.10        12.95        12.30        27.42        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IP-7968 TCGA-KB-A6F7 TCGA-RD-A7BT 
       13.08         1.41         2.53        60.56         8.61 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.07     0.07     3.25     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  116.38    79.07   122.30    19.36    72.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  11.505   11.700    6.345   14.010   11.770 
[1] "0.1 - 116.4 (11.5)" "0.1 - 79.1 (11.7)"  "0.1 - 122.3 (6.3)" 
[4] "3.2 - 19.4 (14.0)"  "0.1 - 72.2 (11.8)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        3       18       10        16        22         2
  subtype2       0        3        3        2         3         2         0
  subtype3       0        0        3        8         4        10         1
  subtype4       1        1        1        0         1         0         0
  subtype5       0        5       13        7         8        13         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         24         26         17       13
  subtype2          7          5          1        3
  subtype3         14          6          8        6
  subtype4          2          2          1        0
  subtype5         14          6          5        9
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        0        1        0
  STAGE IA          3        3        0        1        5
  STAGE IB         18        3        3        1       13
  STAGE II         10        2        8        0        7
  STAGE IIA        16        3        4        1        8
  STAGE IIB        22        2       10        0       13
  STAGE III         2        0        1        0        0
  STAGE IIIA       24        7       14        2       14
  STAGE IIIB       26        5        6        2        6
  STAGE IIIC       17        1        8        1        5
  STAGE IV         13        3        6        0        9
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  6 36 66 47
  subtype2  3  9 16  2
  subtype3  2 13 28 17
  subtype4  2  4  1  2
  subtype5  7 23 35 17
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        3        2        2        7
  T2       36        9       13        4       23
  T3       66       16       28        1       35
  T4       47        2       17        2       17
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 48 43 29 34
  subtype2 11  1  9  8
  subtype3 14 22 17  9
  subtype4  3  1  2  3
  subtype5 33 25  9 13
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       48       11       14        3       33
  N1       43        1       22        1       25
  N2       29        9       17        2        9
  N3       34        8        9        3       13
[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 140  12   8
  subtype2  29   1   0
  subtype3  56   4   2
  subtype4  10   0   0
  subtype5  73   4   7
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0      140       29       56       10       73
  M1       12        1        4        0        4
  MX        8        0        2        0        7
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 72 88
  subtype2  9 21
  subtype3 24 38
  subtype4  6  4
  subtype5 26 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   88
  subtype2    9   21
  subtype3   24   38
  subtype4    6    4
  subtype5   26   58
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       72        9       24        6       26
  MALE         88       21       38        4       58
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    39
  subtype2                                     4
  subtype3                                    12
  subtype4                                     3
  subtype5                                     4
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     71
  subtype2                                                     10
  subtype3                                                     30
  subtype4                                                      3
  subtype5                                                     40
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                20
  subtype2                                                                 8
  subtype3                                                                 8
  subtype4                                                                 2
  subtype5                                                                16
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               16
  subtype2                                                4
  subtype3                                                8
  subtype4                                                2
  subtype5                                               15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                       10
  subtype2                                                        2
  subtype3                                                        3
  subtype4                                                        0
  subtype5                                                        4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         1
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
D1V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  71
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus         0   1
  subtype1   1 159
  subtype2   0  30
  subtype3   2  60
  subtype4   1   9
  subtype5   3  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  159
  subtype2    0   30
  subtype3    2   60
  subtype4    1    9
  subtype5    3   81
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        0        2        1        3
  YES      159       30       60        9       81
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 129   5   6  13
  subtype2  24   3   1   1
  subtype3  49   2   2   5
  subtype4   9   0   0   1
  subtype5  66   3   4   5
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      129       24       49        9       66
  R1        5        3        2        0        3
  R2        6        1        2        0        4
  RX       13        1        5        1        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    38                         1
  subtype2     3                         0
  subtype3    17                         0
  subtype4     4                         0
  subtype5    22                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   102
  subtype2                                         0    19
  subtype3                                         0    37
  subtype4                                         0     4
  subtype5                                         1    46
D1V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           38        3       17        4
  BLACK OR AFRICAN AMERICAN                        1        0        0        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        0
  WHITE                                          102       19       37        4
                                           clus
vv                                          subtype5
  ASIAN                                           22
  BLACK OR AFRICAN AMERICAN                        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           46
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 89 20
  subtype2 58 26
  subtype3 65 34
subtype1 subtype2 subtype3 
     109       84       99 
subtype1 subtype2 subtype3 
      20       26       34 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 
        5.62        11.70        34.68        13.12         7.00        32.78 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 
       30.90        32.94        24.76        23.93         0.69        12.43 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       12.76        18.71        12.26        20.55         0.72        12.95 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        7.40         6.18        19.50        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        3.32        19.17         0.69         0.26        15.85         1.12 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44U 
       15.81        13.45         7.53        16.44        15.68         1.15 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PE 
        2.27         0.92        12.89         0.53        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8524 TCGA-CD-8528 
        1.15        13.64        11.57         5.13         0.07         0.10 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.10         0.13         0.07         0.10         0.10 
TCGA-CG-4437 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        8.05         0.99         6.02        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-8573 
       21.07        12.36        17.85        13.35        15.22        19.50 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY 
       16.44         5.92        15.16        13.78        14.76        11.44 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 
        9.76         7.40         6.58        14.47        21.27        19.53 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 
       11.08         1.55        18.08         1.51        14.27        11.41 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.10        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
        3.25        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-8462 
        2.10        19.36        17.69         9.67         8.88        18.81 
TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-MX-A5UJ 
        3.39         1.41         6.44         6.87         1.81         4.50 
TCGA-RD-A7C1 
       16.67 

$subtype2
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 
        0.62        21.11         9.21        35.24        15.42         0.16 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 
       18.54         0.95         1.32         0.69         0.26         1.55 
TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
        0.36        14.79         5.39         9.21        20.22        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 
       15.81         0.59         0.62        10.68         0.66         0.72 
TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5813 TCGA-CD-8527 TCGA-CD-8533 
       20.65         3.25        13.15         0.39         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
        0.13         0.07         0.13         0.13         0.13         0.10 
TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
       14.01         1.02        15.02        79.07         4.01        55.04 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       12.66        20.55        18.84        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT 
       12.79        11.31        12.33         0.23         6.97        14.27 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       11.24        11.31         2.96        15.65         0.62         7.79 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       16.24        72.23         0.39        17.06        13.58         0.56 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GX 
        5.92        14.17        22.75        25.81        11.77        10.19 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.95        12.30        27.42        21.21        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IP-7968 TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-ZQ-A9CR 
       13.08         5.56         2.53         8.61         8.94         0.79 

$subtype3
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 
       15.95        10.13        13.68        39.12         0.82        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-7196 
       13.22        16.14         1.25         8.98        31.20        12.82 
TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8285 
       28.01         0.69        17.49         0.82         0.49         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       16.31         1.48         0.26        22.19         2.96         0.95 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
        0.36         3.72         0.72        12.79         2.14         0.20 
TCGA-BR-8677 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        0.49        12.56         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-CD-5798 
       14.17        12.82         0.66        19.36         0.46         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 
       13.18         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 
        0.16         0.10         6.97         1.02         0.99       105.07 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 
        7.99        11.93        19.13        18.54        18.61        10.55 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET 
       24.72        16.80        17.19        21.14        20.91        13.71 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        4.34         7.13         8.12         3.02        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 
        5.03         0.23        26.47        12.59        10.62         0.76 
TCGA-HU-A4GJ TCGA-HU-A4GY TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-KB-A6F5 
       21.37         0.26         8.81         3.45         5.36         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       60.56         3.72        11.05         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-ZA-A8F6 
       16.87         5.79         4.21 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
   65.10    79.07   122.30 
subtype1 subtype2 subtype3 
  11.700   10.225   10.130 
[1] "0.1 - 65.1 (11.7)"  "0.1 - 79.1 (10.2)"  "0.1 - 122.3 (10.1)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        7       12        7        13        21         0
  subtype2       0        3        9       10         8        14         0
  subtype3       0        1       11        8        12        11         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         16         18         14        3
  subtype2         19         10          8        7
  subtype3         21         16         10       10
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        0
  STAGE IA          7        3        1
  STAGE IB         12        9       11
  STAGE II          7       10        8
  STAGE IIA        13        8       12
  STAGE IIB        21       14       11
  STAGE III         0        0        2
  STAGE IIIA       16       19       21
  STAGE IIIB       18       10       16
  STAGE IIIC       14        8       10
  STAGE IV          3        7       10
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 11 24 48 30
  subtype2  4 27 38 19
  subtype3  3 20 51 28
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       11        4        3
  T2       24       27       20
  T3       48       38       51
  T4       30       19       28
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 43 26 19 25
  subtype2 29 23 19 17
  subtype3 31 27 22 21
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       29       31
  N1       26       23       27
  N2       19       19       22
  N3       25       17       21
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 111   1   1
  subtype2  75   4   9
  subtype3  88   9   5
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      111       75       88
  M1        1        4        9
  MX        1        9        5
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 43 70
  subtype2 33 55
  subtype3 42 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   70
  subtype2   33   55
  subtype3   42   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       33       42
  MALE         70       55       60
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    19
  subtype2                                     5
  subtype3                                    35
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     51
  subtype2                                                     39
  subtype3                                                     36
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                13
  subtype2                                                                17
  subtype3                                                                15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               20
  subtype2                                               22
  subtype3                                                3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        7
  subtype2                                                        2
  subtype3                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         2
  subtype3                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        0
  subtype3                                        3
D2V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        20
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        22
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   35
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus         0   1
  subtype1   1 112
  subtype2   5  83
  subtype3   1 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  112
  subtype2    5   83
  subtype3    1  101
     clus
vv    subtype1 subtype2 subtype3
  NO         1        5        1
  YES      112       83      101
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2
  subtype1 103   4   1
  subtype2  73   4   3
  subtype3  89   5   2
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      103       73       89
  R1        4        4        5
  R2        1        3        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    34                         2
  subtype2    24                         2
  subtype3    28                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    67
  subtype2                                         1    52
  subtype3                                         0    66
D2V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           34       24       28
  BLACK OR AFRICAN AMERICAN                        2        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           67       52       66
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 51 19
  subtype2 58 27
  subtype3 53 26
subtype1 subtype2 subtype3 
      70       85       79 
subtype1 subtype2 subtype3 
      19       27       26 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
        5.62        11.70         6.97        30.90         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 
       34.68        32.78         1.25         8.98        30.90        32.94 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8285 TCGA-BR-8286 
       12.43         0.95        12.76         1.32         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
        0.26         6.18        19.50         0.26         0.95        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
        0.26        15.85         0.72        15.81        13.45         7.53 
TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       15.81        10.68        13.51         1.15        11.57         5.13 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 
        0.07         0.10         0.13         0.10         0.13         0.13 
TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4469 
        0.07        20.02         1.02         7.99         8.05         7.07 
TCGA-CG-5723 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
      105.07        21.07         7.99        13.35        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A4YX 
       11.31        12.33        24.72        19.50        16.44        15.16 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4GQ 
        7.79        14.47        26.47        11.41        25.81         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IP-7968 
        6.51         6.25        10.19         2.53 

$subtype2
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6456 
        6.61         4.64         7.43         9.57        15.95        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
       13.68         7.00         0.82        13.84        13.22        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       31.20        12.82         9.21         0.69         0.16         0.69 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8291 
       18.71        17.49         0.82         0.49        20.55        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        1.48         7.40         0.36        22.19         2.96        13.74 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8483 
       14.04         3.32         0.36         0.69         3.72         5.39 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       20.22        12.79         0.20         0.49        16.44         0.59 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         0.66         3.02         2.27         0.92        13.41 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI 
       12.89         0.79        12.82        19.36         0.46        13.64 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8530 
        2.83         0.07         0.39         0.07         0.07         0.16 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 
        0.13         0.10         3.02        12.03        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 
       30.97         6.97         1.02         1.02        65.10        11.93 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4Z0 
       19.13        18.54        17.85        16.80        17.19        14.76 
TCGA-F1-A448 TCGA-FP-7916 TCGA-HU-8610 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.27         3.02         0.76        19.36        17.69        12.30 
TCGA-IN-8462 
       18.81 

$subtype3
TCGA-BR-4191 TCGA-BR-6455 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-7703 TCGA-BR-7704 
       18.35        13.12         0.62        16.14        24.76        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 
       15.42        28.01        18.54         0.72         1.55         4.31 
TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U 
        9.21         2.14        11.54        15.68         0.62         1.15 
TCGA-BR-A4IV TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PD 
       13.51         0.72        14.17         0.53         0.66        20.65 
TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 
       20.42         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.13         0.10         0.07         0.13         0.13 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-4443 
        0.10         0.10        27.02        15.95        54.08        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5720 
       47.05        19.07        21.99         9.01        18.97         0.99 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02        12.03        15.02        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       55.04        12.36        12.66        20.55        18.84        18.61 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT 
       10.26        12.79        10.55         0.23        21.14        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7998 
        5.92        13.78        16.24         6.58        72.23        22.29 
TCGA-HU-8608 TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       10.62         0.26        12.95        27.42        21.21         3.45 
TCGA-IN-8663 
        3.39 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  105.07    65.10    79.07 
subtype1 subtype2 subtype3 
   9.585    9.210   12.790 
[1] "0.1 - 105.1 (9.6)" "0.1 - 65.1 (9.2)"  "0.1 - 79.1 (12.8)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        9        4        10        10         1
  subtype2       0        2        3       12        10        15         1
  subtype3       2        4       13       12         5        11         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         16         12          8        6
  subtype2         13         11         11       10
  subtype3         11         11          5        9
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        2
  STAGE IA          0        2        4
  STAGE IB          9        3       13
  STAGE II          4       12       12
  STAGE IIA        10       10        5
  STAGE IIB        10       15       11
  STAGE III         1        1        1
  STAGE IIIA       16       13       11
  STAGE IIIB       12       11       11
  STAGE IIIC        8       11        5
  STAGE IV          6       10        9
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0 20 39 20
  subtype2  2 16 37 33
  subtype3  6 31 29 21
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        2        6
  T2       20       16       31
  T3       39       37       29
  T4       20       33       21
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 27 22 14 15
  subtype2 26 28 15 20
  subtype3 34 23 13 15
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       27       26       34
  N1       22       28       23
  N2       14       15       13
  N3       15       20       15
[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 72  4  6
  subtype2 84  6  1
  subtype3 81  6  4
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       72       84       81
  M1        4        6        6
  MX        6        1        4
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 34 48
  subtype2 38 53
  subtype3 28 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   48
  subtype2   38   53
  subtype3   28   63
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       38       28
  MALE         48       53       63
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     9
  subtype2                                    19
  subtype3                                    14
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     45
  subtype2                                                     43
  subtype3                                                     47
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                13
  subtype2                                                                 9
  subtype3                                                                15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               11
  subtype2                                                4
  subtype3                                               11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                       12
  subtype3                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         2
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        1
  subtype3                                        0
D3V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  43
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1  2 80
  subtype2  0 91
  subtype3  5 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    0   91
  subtype3    5   86
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        5
  YES       80       91       86
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 64  3  1 11
  subtype2 72  4  2  7
  subtype3 69  2  5  7
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       64       72       69
  R1        3        4        2
  R2        1        2        5
  RX       11        7        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    15                         0    57
  subtype2    23                         0    57
  subtype3    22                         2    45
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           15       23       22
  BLACK OR AFRICAN AMERICAN        0        0        2
  WHITE                           57       57       45
[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(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 26  6
  subtype2 49 23
  subtype3 34 11
  subtype4 53 32
subtype1 subtype2 subtype3 subtype4 
      32       72       45       85 
subtype1 subtype2 subtype3 subtype4 
       6       23       11       32 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6710 TCGA-BR-6802 
        5.62        11.70        30.90         6.18         8.98        30.90 
TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8382 TCGA-BR-8690 TCGA-BR-A4PF 
       32.94        20.55         0.26        15.85        10.68         1.15 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 
        0.10         0.13        20.02         7.99         8.05        12.03 
TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
        1.02       105.07        21.07        15.98        11.31        12.33 
TCGA-D7-A4YU TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-8610 TCGA-HU-A4GF TCGA-HU-A4H3 
       16.44        14.47        21.27         0.76        25.81        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 
       17.69        12.30 

$subtype2
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7723 
        6.61        18.35        15.95        13.12        16.14        18.54 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8483 
        1.32        16.31         1.55         7.40         4.31         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-A44U TCGA-BR-A452 
        0.72         9.21        20.22         0.49         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        3.02         2.27        13.51         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.53        20.65        20.42         3.25        13.15         0.30 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A4MH 
        0.39         0.07         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 
        0.10         3.02        27.02        15.95         1.02        54.08 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        21.99         9.01        18.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99         6.02        15.02        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6817 TCGA-D7-6818 
       55.04        12.66        20.55        18.61        12.79        10.55 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-EQ-A4SO 
       17.19         0.23        21.14        14.27         7.79        16.24 
TCGA-HJ-7597 TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       26.47         0.26        12.95        27.42        21.21         3.45 

$subtype3
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7703 
        6.97         6.61        34.68        32.78         1.25        24.76 
TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8372 
       35.24        12.95         6.18        19.50         0.95        19.17 
TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4QL 
        0.26        15.81        11.54        15.81        13.51        11.57 
TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
        5.13        13.18         0.07         0.10         0.13         0.10 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4469 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 
        0.07         0.10         7.07        12.03         7.99        12.36 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A4YY 
       13.35        15.22        24.72        19.50        15.16        13.78 
TCGA-F1-6177 TCGA-F1-6875 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GT 
        6.58        72.23        11.41        10.62         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IP-7968 
        6.25        10.19         2.53 

$subtype4
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        4.64         7.43         9.57        10.13        13.68         7.00 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 
        0.82         0.62        13.84        13.22        21.11        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        15.42        28.01         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8362 
        0.82         0.49         0.72         0.26         1.48         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19         2.96        13.74        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        0.36         0.69         3.72        12.79         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.20         7.53        16.44         0.59        15.68         0.62 
TCGA-BR-A44T TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.56         0.92        13.41        12.89        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8525 
       19.36         0.46        13.64         2.83         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.16         0.10         0.13         0.13         0.13 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5728 
       12.00        22.98        30.97         6.97         1.02        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6527 
       11.93        19.13        18.84        18.54        17.85        10.26 
TCGA-D7-8572 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-FP-7916 TCGA-FP-7998 TCGA-IN-8462 
       16.80         5.92        14.76         3.02        22.29        18.81 
TCGA-IN-8663 
        3.39 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  105.07    79.07    72.23    65.10 
subtype1 subtype2 subtype3 subtype4 
  12.315   11.605   11.410    7.530 
[1] "0.1 - 105.1 (12.3)" "0.1 - 79.1 (11.6)"  "0.1 - 72.2 (11.4)" 
[4] "0.1 - 65.1 (7.5)"  
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        7        4         3         4         0
  subtype2       0        3       10       11         4         9         1
  subtype3       2        2        4        3         7         4         1
  subtype4       0        0        4       10        11        19         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          5          5          3        0
  subtype2         14         10          2       14
  subtype3         11          8          5        3
  subtype4         10         11         14        8
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        2        0
  STAGE IA          1        3        2        0
  STAGE IB          7       10        4        4
  STAGE II          4       11        3       10
  STAGE IIA         3        4        7       11
  STAGE IIB         4        9        4       19
  STAGE III         0        1        1        1
  STAGE IIIA        5       14       11       10
  STAGE IIIB        5       10        8       11
  STAGE IIIC        3        2        5       14
  STAGE IV          0       14        3        8
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 16  9  7
  subtype2  3 27 27 23
  subtype3  4  8 31 10
  subtype4  0 16 38 34
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        3        4        0
  T2       16       27        8       16
  T3        9       27       31       38
  T4        7       23       10       34
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 14  6  6  6
  subtype2 27 24 13 15
  subtype3 19 15  8 10
  subtype4 27 28 15 19
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       14       27       19       27
  N1        6       24       15       28
  N2        6       13        8       15
  N3        6       15       10       19
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 34  0  0
  subtype2 70 10  4
  subtype3 48  2  5
  subtype4 85  4  2
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       34       70       48       85
  M1        0       10        2        4
  MX        0        4        5        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 14 20
  subtype2 28 56
  subtype3 22 33
  subtype4 36 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   20
  subtype2   28   56
  subtype3   22   33
  subtype4   36   55
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       14       28       22       36
  MALE         20       56       33       55
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     4
  subtype2                                    15
  subtype3                                     8
  subtype4                                    15
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     14
  subtype2                                                     40
  subtype3                                                     32
  subtype4                                                     49
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 6
  subtype2                                                                13
  subtype3                                                                 7
  subtype4                                                                11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                7
  subtype2                                                8
  subtype3                                                7
  subtype4                                                4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        5
  subtype3                                                        0
  subtype4                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         1
  subtype3                                                         1
  subtype4                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        2
  subtype3                                        0
  subtype4                                        0
D4V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1  0 34
  subtype2  6 78
  subtype3  0 55
  subtype4  1 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    6   78
  subtype3    0   55
  subtype4    1   90
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        6        0        1
  YES       34       78       55       90
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 30  0  0  3
  subtype2 60  2  7  7
  subtype3 41  2  1  9
  subtype4 74  5  0  6
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       30       60       41       74
  R1        0        2        2        5
  R2        0        7        1        0
  RX        3        7        9        6
[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"
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         0    20
  subtype2    21                         0    39
  subtype3    14                         2    34
  subtype4    18                         0    66
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            7       21       14       18
  BLACK OR AFRICAN AMERICAN        0        0        2        0
  WHITE                           20       39       34       66
[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 53  8
  subtype2 36 22
  subtype3 26 11
  subtype4 24  8
  subtype5 37 18
subtype1 subtype2 subtype3 subtype4 subtype5 
      61       58       37       32       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       22       11        8       18 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6707 
        5.62        11.70        30.90        34.68        32.78        16.14 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 
       30.90        32.94        23.93        12.76        12.26        20.55 
TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 
       12.95        19.50         0.26         0.95         4.31        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
        0.26        15.85         1.12        15.81        13.45        15.81 
TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8531 
       12.89         0.53        20.42        13.18         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4477 
        0.10         0.13         0.07         0.10        15.95        30.97 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-5577 TCGA-D7-6524 
        6.97         6.02       105.07        12.03        12.36        17.85 
TCGA-D7-6525 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-FP-8099 
       13.35        24.72        19.50        15.16        13.78        17.06 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 
       11.08        11.41        12.10        10.62         0.76        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 
       11.84        29.98         2.10        19.36        17.69        18.81 
TCGA-IN-8663 
        3.39 

$subtype2
TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        4.64         9.57        13.12        10.13        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
        0.82        13.84        13.22        21.11        31.20        12.82 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 
        0.69        18.71         0.82         0.49         0.72         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
        0.36        22.19         2.96        13.74        14.04         0.36 
TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
        0.69         3.72         2.14         0.20         0.49        16.44 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       15.68        12.56         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       14.17        12.82        19.36        13.51         0.46         2.83 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 
        0.07         0.39         0.13         0.13         0.10        12.00 
TCGA-D7-6518 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-FP-7916 
       19.13        17.19        20.91        16.44         5.92         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY 
       22.29        59.54         5.03         0.26 

$subtype3
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6710 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-8058 
       18.35         6.18         8.98         0.69         0.16        17.49 
TCGA-BR-8291 TCGA-BR-8484 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-8529 TCGA-CD-8532 
       16.31         0.72         0.66        20.65         0.13         0.10 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5726 
        3.02         1.02         8.05         1.02         0.99        28.96 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8575 
       55.04         7.99        18.54        10.26        12.79         0.23 
TCGA-D7-8576 TCGA-EQ-A4SO TCGA-FP-8211 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 
        6.97        16.24        13.58        24.30         5.59        24.20 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 
        3.25        21.37         8.98        10.19        12.95         9.67 
TCGA-HU-A4HB 
        8.81 

$subtype4
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8486 
        6.61        15.95         0.62        24.76        12.43        20.22 
TCGA-BR-8588 TCGA-BR-8683 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CG-4304 
       12.79         0.59         1.15        13.64         3.25        27.02 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5720 
        7.99        14.01        47.05         9.01         7.07         0.99 
TCGA-D7-5578 TCGA-D7-6522 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4Z0 TCGA-F1-6177 
       12.66        18.61        15.22        15.98        14.76         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-A4GT 
       14.47        21.27        19.53         1.51        14.27         6.51 
TCGA-HU-A4H8 TCGA-IN-7806 
        8.88        21.21 

$subtype5
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
        7.00         1.25         9.21        15.42        28.01        18.54 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 
        0.95         1.32         0.69         0.26        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 
        9.21        11.54         0.62         0.66         0.92         0.72 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
       13.15         0.07         0.07         0.16         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        0.07         0.10        54.08         4.01        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6519 
       21.99        18.97        22.98         1.02        15.02        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.84        17.19        10.55        11.31        12.33        16.80 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8631 
       21.14        14.27         7.79        72.23         0.39         0.56 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
       25.81        11.77         6.25        12.30        27.42         3.45 
TCGA-IP-7968 
        2.53 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.07     0.10     0.59     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  105.07    59.54    55.04    47.05    72.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.950    9.850    8.980   13.215    9.210 
[1] "0.1 - 105.1 (12.9)" "0.1 - 59.5 (9.9)"   "0.1 - 55.0 (9.0)"  
[4] "0.6 - 47.0 (13.2)"  "0.1 - 72.2 (9.2)"  
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2        8        6        12        11         0
  subtype2       0        0        1        5         7         9         1
  subtype3       0        2        3        4         2         7         0
  subtype4       2        3        8        1         3         7         1
  subtype5       0        3        7        7         5         9         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          8          6          6        3
  subtype2          9         12         10        6
  subtype3          7          5          3       10
  subtype4          5          3          0        3
  subtype5         11          6          4        5
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        0        2        0
  STAGE IA          2        0        2        3        3
  STAGE IB          8        1        3        8        7
  STAGE II          6        5        4        1        7
  STAGE IIA        12        7        2        3        5
  STAGE IIB        11        9        7        7        9
  STAGE III         0        1        0        1        1
  STAGE IIIA        8        9        7        5       11
  STAGE IIIB        6       12        5        3        6
  STAGE IIIC        6       10        3        0        4
  STAGE IV          3        6       10        3        5
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 19 24 18
  subtype2  0  5 30 25
  subtype3  3 13 16 13
  subtype4  6 15  8  8
  subtype5  2 18 29 11
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        0        3        6        2
  T2       19        5       13       15       18
  T3       24       30       16        8       29
  T4       18       25       13        8       11
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 30 17  8  9
  subtype2 14 19  8 19
  subtype3 10 15 11  8
  subtype4 17  7  9  3
  subtype5 20 18 10 10
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       30       14       10       17       20
  N1       17       19       15        7       18
  N2        8        8       11        9       10
  N3        9       19        8        3       10
[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 63  2  1
  subtype2 58  3  2
  subtype3 35  7  4
  subtype4 34  2  1
  subtype5 53  4  5
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       63       58       35       34       53
  M1        2        3        7        2        4
  MX        1        2        4        1        5
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 28 38
  subtype2 25 38
  subtype3 18 28
  subtype4 14 23
  subtype5 20 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   38
  subtype2   25   38
  subtype3   18   28
  subtype4   14   23
  subtype5   20   42
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       28       25       18       14       20
  MALE         38       38       28       23       42
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    12
  subtype2                                    19
  subtype3                                    10
  subtype4                                     5
  subtype5                                     5
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     42
  subtype2                                                     28
  subtype3                                                     19
  subtype4                                                     13
  subtype5                                                     29
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 3
  subtype2                                                                 4
  subtype3                                                                 6
  subtype4                                                                 7
  subtype5                                                                14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                8
  subtype2                                                3
  subtype3                                                7
  subtype4                                                8
  subtype5                                               10
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
  subtype4                                                         0
  subtype5                                                         0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        7
  subtype3                                                        3
  subtype4                                                        3
  subtype5                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         1
  subtype5                                                         2
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
D5V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus        0  1
  subtype1  0 66
  subtype2  0 63
  subtype3  5 41
  subtype4  0 37
  subtype5  2 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    0   63
  subtype3    5   41
  subtype4    0   37
  subtype5    2   60
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         0        0        5        0        2
  YES       66       63       41       37       60
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 55  1  1  5
  subtype2 47  2  0  6
  subtype3 35  2  5  4
  subtype4 30  1  2  3
  subtype5 49  3  2  4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       55       47       35       30       49
  R1        1        2        2        1        3
  R2        1        0        5        2        2
  RX        5        6        4        3        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"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                         1    38
  subtype2    19                         0    43
  subtype3    13                         0    19
  subtype4     6                         1    21
  subtype5    15                         2    35
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20       19       13        6       15
  BLACK OR AFRICAN AMERICAN        1        0        0        1        2
  WHITE                           38       43       19       21       35
[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(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 22 12
  subtype2 16  4
  subtype3 29 18
  subtype4 37 15
  subtype5 29 10
  subtype6 26  8
  subtype7 17  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      34       20       47       52       39       34       17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      12        4       18       15       10        8        0 
$subtype1
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7717 TCGA-BR-8059 
        5.62        30.90         7.00         1.25         0.69         0.82 
TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8590 TCGA-BR-A4IY TCGA-BR-A4J6 
        0.26         0.26         0.95         2.14        12.89         0.66 
TCGA-CD-5798 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A487 TCGA-CD-A48C 
        2.83         0.07         0.16         0.10         0.13         0.13 
TCGA-CD-A4MI TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.10        19.07        12.00        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 
        1.02         6.02       105.07        12.03        20.55        13.35 
TCGA-D7-A4YU TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       16.44        21.21        18.81         3.39 

$subtype2
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-7196 TCGA-BR-7958 
       11.70        13.12        13.22        16.14        12.82        12.76 
TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-A4J4 TCGA-CD-5801 TCGA-D7-5577 
        0.26        15.81        15.68         0.53        13.18        12.36 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-FP-7998 TCGA-HU-8608 TCGA-HU-A4G2 
       24.72        19.50        15.16        22.29        10.62        24.30 
TCGA-HU-A4G6 TCGA-HU-A4H0 
       12.30         2.10 

$subtype3
TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        4.64         9.57        15.95        13.68        39.12         0.82 
TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       13.84        31.20         0.69         0.49         0.72        16.31 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
        7.40        22.19         2.96        13.74        14.04         0.36 
TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8592 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
        0.69         3.72         0.20        16.44        12.56         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 
       13.41        13.51         0.79        14.17        12.82        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-A489 TCGA-D7-6518 
       13.51         0.46         0.07         0.39         0.13        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4Z0 
       18.61        17.85        17.19        20.91         5.92        14.76 
TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY TCGA-IN-7808 
        3.02        59.54         5.03         0.26         3.45 

$subtype4
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-7722 
       18.35         6.18        34.68         8.98        30.90         0.16 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8687 TCGA-BR-A4PD 
        0.95        17.49         0.72        12.79         0.62        20.65 
TCGA-BR-A4PE TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8536 TCGA-CG-4301 TCGA-CG-4304 
       20.42         0.13         0.10         0.10         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5722 
       15.95         1.02         8.05        21.99         1.02         0.99 
TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6817 
       28.96        55.04         7.99        18.54        10.26        12.79 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-EQ-A4SO TCGA-FP-7735 
       11.31         0.23         6.97        21.14        16.24         0.39 
TCGA-FP-8211 TCGA-HU-8238 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       13.58         1.51         0.76         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 
        3.25        11.77        21.37         8.98        10.19        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       17.69         9.67         8.88         8.81 

$subtype5
TCGA-BR-4280 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7703 TCGA-BR-8362 
        6.61         0.62        32.78        21.11        24.76         0.36 
TCGA-BR-8368 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4PF 
        4.31        20.22         1.12        15.81         0.59         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8528 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 
       13.64         3.25         0.10         0.07         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
        4.01        14.01        47.05         9.01        18.97         7.07 
TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-EQ-8122 
        0.99        12.66        17.19        15.22        15.98         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HU-8244 TCGA-HU-8604 
        6.58        14.47        19.53        11.08        14.27        12.10 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81         6.51         6.25 

$subtype6
TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       10.13         9.21        15.42        28.01        18.54        18.71 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 
        1.32         0.69        14.79         5.39         9.21        11.54 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8533 
        0.66         0.92         0.72        13.15         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4443 TCGA-CG-5725 TCGA-D7-6520 
        0.13         0.07         0.10        29.98        15.02        18.84 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-F1-6875 TCGA-FP-8099 
       10.55        12.33        16.80        14.27        72.23        17.06 
TCGA-FP-8631 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IP-7968 
        0.56        12.30        27.42         2.53 

$subtype7
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 
       32.94        23.93        12.43        12.26        20.55        12.95 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8677 TCGA-CD-A4MJ 
       19.50        19.17        15.85        13.45         0.49         0.10 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4H3 
       13.78        21.27        11.41        29.98        19.36 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.26     0.07     0.10     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  105.07    24.72    59.54    55.04    54.08    72.23    32.94 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   4.505   13.150   12.560    9.930   11.080   11.045   15.850 
[1] "0.1 - 105.1 (4.5)" "0.3 - 24.7 (13.1)" "0.1 - 59.5 (12.6)"
[4] "0.1 - 55.0 (9.9)"  "0.1 - 54.1 (11.1)" "0.1 - 72.2 (11.0)"
[7] "0.1 - 32.9 (15.8)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        2        6         2         8         1
  subtype2       0        1        1        0         2         4         0
  subtype3       0        0        2        5         7         8         1
  subtype4       0        4        8        7         3        10         0
  subtype5       2        3        7        1         9         5         1
  subtype6       0        2        4        3         4         4         0
  subtype7       0        0        3        1         2         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          3          4          1        7
  subtype2          4          6          2        1
  subtype3          7          8          7        4
  subtype4          9          5          4        9
  subtype5          4          3          1        5
  subtype6         12          3          3        1
  subtype7          1          3          5        0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           0        0        0        0        2        0        0
  STAGE IA          0        1        0        4        3        2        0
  STAGE IB          2        1        2        8        7        4        3
  STAGE II          6        0        5        7        1        3        1
  STAGE IIA         2        2        7        3        9        4        2
  STAGE IIB         8        4        8       10        5        4        4
  STAGE III         1        0        1        0        1        0        0
  STAGE IIIA        3        4        7        9        4       12        1
  STAGE IIIB        4        6        8        5        3        3        3
  STAGE IIIC        1        2        7        4        1        3        5
  STAGE IV          7        1        4        9        5        1        0
[1] 11  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       T1 T2 T3 T4
  subtype1  0 10 16 10
  subtype2  1  2 11  7
  subtype3  0  9 23 17
  subtype4  6 21 18 15
  subtype5  5 13 16  8
  subtype6  1 11 18  8
  subtype7  0  4  5 10
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        0        1        0        6        5        1        0
  T2       10        2        9       21       13       11        4
  T3       16       11       23       18       16       18        5
  T4       10        7       17       15        8        8       10
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 10 17  4  4
  subtype2  5  9  2  5
  subtype3 13 12  7 16
  subtype4 18 19 16  7
  subtype5 22  6  9  4
  subtype6 13 10  7  6
  subtype7 10  3  1  7
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       10        5       13       18       22       13       10
  N1       17        9       12       19        6       10        3
  N2        4        2        7       16        9        7        1
  N3        4        5       16        7        4        6        7
[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 34  3  1
  subtype2 19  1  1
  subtype3 45  4  1
  subtype4 51  7  4
  subtype5 37  3  2
  subtype6 36  0  4
  subtype7 21  0  0
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       34       19       45       51       37       36       21
  M1        3        1        4        7        3        0        0
  MX        1        1        1        4        2        4        0
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 17 21
  subtype2  2 19
  subtype3 22 28
  subtype4 24 38
  subtype5 19 23
  subtype6 10 30
  subtype7 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   21
  subtype2    2   19
  subtype3   22   28
  subtype4   24   38
  subtype5   19   23
  subtype6   10   30
  subtype7   11   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       17        2       22       24       19       10       11
  MALE         21       19       28       38       23       30       10
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     8
  subtype2                                     5
  subtype3                                    22
  subtype4                                     9
  subtype5                                     4
  subtype6                                     1
  subtype7                                     2
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     19
  subtype2                                                     11
  subtype3                                                     17
  subtype4                                                     29
  subtype5                                                     16
  subtype6                                                     24
  subtype7                                                     15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 6
  subtype2                                                                 0
  subtype3                                                                 3
  subtype4                                                                 7
  subtype5                                                                10
  subtype6                                                                 6
  subtype7                                                                 2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                1
  subtype2                                                4
  subtype3                                                1
  subtype4                                               13
  subtype5                                               10
  subtype6                                                6
  subtype7                                                1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         1
  subtype5                                                         0
  subtype6                                                         0
  subtype7                                                         0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        0
  subtype3                                                        6
  subtype4                                                        3
  subtype5                                                        1
  subtype6                                                        1
  subtype7                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         1
  subtype6                                                         2
  subtype7                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
  subtype4                                        0
  subtype5                                        0
  subtype6                                        0
  subtype7                                        0
D6V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype7
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1  0 38
  subtype2  0 21
  subtype3  0 50
  subtype4  5 57
  subtype5  0 42
  subtype6  2 38
  subtype7  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   38
  subtype2    0   21
  subtype3    0   50
  subtype4    5   57
  subtype5    0   42
  subtype6    2   38
  subtype7    0   21
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        0        0        5        0        2        0
  YES       38       21       50       57       42       38       21
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 27  1  1  5
  subtype2 20  0  0  1
  subtype3 37  3  1  3
  subtype4 48  3  6  4
  subtype5 34  1  2  2
  subtype6 33  1  0  4
  subtype7 17  0  0  3
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       27       20       37       48       34       33       17
  R1        1        0        3        3        1        1        0
  R2        1        0        1        6        2        0        0
  RX        5        1        3        4        2        4        3
[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"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     8                         0    21
  subtype2     7                         0    14
  subtype3    15                         0    34
  subtype4    19                         1    25
  subtype5    10                         2    20
  subtype6    10                         1    26
  subtype7     4                         0    16
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            8        7       15       19       10
  BLACK OR AFRICAN AMERICAN        0        0        0        1        2
  WHITE                           21       14       34       25       20
                           clus
vv                          subtype6 subtype7
  ASIAN                           10        4
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                           26       16
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 68 32
  subtype2 61 36
  subtype3 95 24
subtype1 subtype2 subtype3 
     100       97      119 
subtype1 subtype2 subtype3 
      32       36       24 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         6.61         6.97        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        6.18         6.61        34.68        15.95        13.12         7.00 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7958 
       32.78        16.14         1.25        30.90        32.94        12.76 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       12.26        20.55         0.72        12.95        16.31         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
        6.18        19.50         0.36         0.26         0.95        19.17 
TCGA-BR-8483 TCGA-BR-8589 TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        5.39        15.81         5.13         3.25        13.18         0.30 
TCGA-CD-5813 TCGA-CD-8531 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4301 
        0.39         0.10         0.13         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        47.05        12.03         9.01 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
        4.01        21.07         7.99        12.36        12.66        20.55 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-EQ-5647 
       24.72        17.19        15.16        13.78         9.76         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8238 
        6.58        14.47        21.27        13.58        26.47         1.51 
TCGA-HU-8244 TCGA-HU-A4G3 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 
       14.27         5.59        29.98         6.25        10.19        17.69 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A7NU 
        3.45        18.81         3.39         1.81 

$subtype2
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        4.64         7.43         9.57        10.13        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 
        0.82         0.62        13.84        13.22         8.98        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       31.20        12.82         0.16        12.43         0.95         0.69 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 
       18.71        17.49         0.82         0.49         0.26         7.40 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         2.96        13.74        14.04         3.32         0.36 
TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        0.69         3.72        12.79         2.14        13.45         0.20 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
        0.49        16.44         0.59        15.68        12.56         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         0.79        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 
        0.66        19.36        13.51         0.46        13.64         2.83 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A4MI 
        0.07         0.13         0.16         0.10         0.13         0.10 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 
       12.00         6.97        65.10        55.04        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8578 
       18.84        18.54        18.61        10.55        16.80        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       20.91        16.44        14.76        13.71        11.31        11.44 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        4.34         7.13         7.79         3.02        22.29        59.54 
TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-MX-A5UG TCGA-RD-A7BS 
        5.03        21.37         0.10         0.26         3.72        11.05 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.67        40.64       115.69       116.38        71.38        57.44 
TCGA-ZA-A8F6 
        4.21 

$subtype3
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8285 TCGA-BR-8295 
        0.69        18.54         1.32         0.69         0.26         1.55 
TCGA-BR-8368 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8485 
        4.31        14.79         0.26        15.85         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8687 
       20.22         1.12         7.53        11.54        15.81         0.62 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       10.68         1.15         0.66         2.27         0.92        12.89 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5800 
        0.72        20.65        20.42         1.15        11.57        13.15 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MH 
        0.13         0.10         0.07         0.13         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-6527 
        0.10        19.07        21.99        18.97        15.02        10.26 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT 
       11.31        12.33        19.50         0.23         6.97        14.27 
TCGA-D7-A4YV TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO 
        5.92        11.24         2.96        15.65         7.40        16.24 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
       72.23         8.12         0.39        19.53        17.06         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 
       11.08         1.55         0.23        18.08         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
       11.77         8.98         6.51         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ 
        6.87         5.56         2.53         5.56        60.56         4.50 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       16.67       122.30        37.91         8.94         5.79 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  105.07   116.38   122.30 
subtype1 subtype2 subtype3 
   12.51    11.31     9.21 
[1] "0.1 - 105.1 (12.5)" "0.1 - 116.4 (11.3)" "0.1 - 122.3 (9.2)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        3       11       11        10        15         2
  subtype2       0        0        8        8         9        15         1
  subtype3       1        9       19        9        14        17         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         21          9          7       16
  subtype2         15         21         12       10
  subtype3         25         15         13        4
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        0        1
  STAGE IA          3        0        9
  STAGE IB         11        8       19
  STAGE II         11        8        9
  STAGE IIA        10        9       14
  STAGE IIB        15       15       17
  STAGE III         2        1        0
  STAGE IIIA       21       15       25
  STAGE IIIB        9       21       15
  STAGE IIIC        7       12       13
  STAGE IV         16       10        4
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  5 37 48 21
  subtype2  0 20 45 35
  subtype3 15 28 54 29
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        0       15
  T2       37       20       28
  T3       48       45       54
  T4       21       35       29
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 32 34 25 18
  subtype2 28 26 19 27
  subtype3 51 32 22 21
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       32       28       51
  N1       34       26       32
  N2       25       19       22
  N3       18       27       21
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  98  13   6
  subtype2  93   6   4
  subtype3 118   2   7
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       98       93      118
  M1       13        6        2
  MX        6        4        7
[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 48 69
  subtype2 38 65
  subtype3 51 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   69
  subtype2   38   65
  subtype3   51   76
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       48       38       51
  MALE         69       65       76
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    16
  subtype2                                    34
  subtype3                                    12
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     59
  subtype2                                                     39
  subtype3                                                     57
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                25
  subtype2                                                                 9
  subtype3                                                                19
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               12
  subtype2                                                8
  subtype3                                               25
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                       11
  subtype3                                                        6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         5
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        1
  subtype3                                        2
D7V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        12
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   34
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1   1 116
  subtype2   2 101
  subtype3   4 123
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  116
  subtype2    2  101
  subtype3    4  123
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        4
  YES      116      101      123
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  78   4  11  18
  subtype2  86   4   0   6
  subtype3 114   5   1   1
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       78       86      114
  R1        4        4        5
  R2       11        0        1
  RX       18        6        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"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    14                         1    69
  subtype2    25                         0    72
  subtype3    46                         3    67
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           14       25       46
  BLACK OR AFRICAN AMERICAN        1        0        3
  WHITE                           69       72       67
[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 110  41
  subtype2  48  25
  subtype3  66  26
subtype1 subtype2 subtype3 
     151       73       92 
subtype1 subtype2 subtype3 
      41       25       26 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         6.61         6.97        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        6.18         6.61        34.68        15.95        13.12         7.00 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 
       32.78        16.14         1.25         8.98        30.90        32.94 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 
       24.76        35.24        23.93         0.16        12.43        12.76 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       17.49        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
       16.31         1.48         6.18         0.26         0.95        19.17 
TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
       15.85         0.72        20.22        15.81        13.45         7.53 
TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IZ TCGA-BR-A4J4 
       15.81         1.15         2.27         0.92         0.79         0.53 
TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
        0.66        20.42         1.15        11.57         5.13         3.25 
TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A48C 
       13.18         0.39         0.10         0.10         0.10         0.13 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
        0.07         0.10         3.02        27.02         7.99         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        47.05        12.03         9.01         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       30.97         6.97         0.99         6.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       28.96         4.01        21.07         7.99        12.36        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.22        12.79 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        19.50        17.19         0.23         6.97        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 
       15.16        13.78        14.76        11.24         9.76        15.65 
TCGA-D7-A748 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       19.53        13.58        11.08         1.55         0.23        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7808 
        0.26         2.10        19.36        17.69         9.67         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81         3.39         5.36         1.41         6.44         6.87 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        1.81         2.53        11.05       122.30        40.64       115.69 
TCGA-RD-A8N5 
       57.44 

$subtype2
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        4.64         7.43         9.57        13.68        39.12         0.82 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7715 
       13.84        13.22        21.11        31.20        12.82        15.42 
TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8364 
        0.69         0.69        18.71         0.49         0.36        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8380 
        2.96        13.74        14.04         3.32         0.36         0.69 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
        3.72         5.39        12.79         0.20         0.49        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.59        15.68        12.56         3.02        13.41        13.51 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
       14.17        12.82        19.36        13.51         0.46        13.64 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 
        2.83         0.07         0.13         0.13         0.10        12.00 
TCGA-CG-4475 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 
       22.98         1.02       105.07        65.10        11.93        19.13 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A74B 
       20.91        16.44        13.71        11.31        11.44         7.13 
TCGA-EQ-5647 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.62         0.39         3.02        22.29        59.54         5.03 
TCGA-HU-A4GQ TCGA-IN-7806 TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 
        0.10        21.21         3.72         4.67       116.38        71.38 
TCGA-ZA-A8F6 
        4.21 

$subtype3
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
       10.13         0.62         9.21        28.01        18.54         0.95 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        0.82         1.32         0.69         0.26         1.55         7.40 
TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8487 
       19.50         4.31        14.79         0.26         9.21         1.12 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4IY 
        2.14        11.54         0.62        10.68         0.66        12.89 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
        0.72        20.65        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.13         0.16         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 
        0.10         0.07         0.13         0.10        20.02        15.95 
TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
        1.02        54.08         4.01        19.07        21.99        18.97 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 
        1.02        15.02        79.07        55.04        12.66        18.84 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.98        10.55        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
       16.80        21.14         5.92         2.96         7.40         7.79 
TCGA-EQ-A4SO TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 
       16.24        17.06         0.56        18.08         5.92        12.59 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 
       14.17        22.75        25.81        11.77        12.95        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        8.88         8.81        27.42        18.38         5.19        13.08 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-RD-A8MW 
        5.56         5.56        60.56         4.50        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.94         5.79 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    79.07 
subtype1 subtype2 subtype3 
   11.41    11.93     9.21 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (11.9)" "0.1 - 79.1 (9.2)"  
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2       11       19       10        17        21         2
  subtype2       0        0        7        5        10         9         0
  subtype3       0        1       12       13         6        17         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         30         21         15       12
  subtype2         12         16          8       10
  subtype3         19          8          9        8
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        0
  STAGE IA         11        0        1
  STAGE IB         19        7       12
  STAGE II         10        5       13
  STAGE IIA        17       10        6
  STAGE IIB        21        9       17
  STAGE III         2        0        1
  STAGE IIIA       30       12       19
  STAGE IIIB       21       16        8
  STAGE IIIC       15        8        9
  STAGE IV         12       10        8
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 15 49 63 38
  subtype2  0 12 40 25
  subtype3  5 24 44 22
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       15        0        5
  T2       49       12       24
  T3       63       40       44
  T4       38       25       22
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 57 42 33 31
  subtype2 24 21 11 22
  subtype3 30 29 22 13
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       57       24       30
  N1       42       21       29
  N2       33       11       22
  N3       31       22       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 150  11   8
  subtype2  72   5   4
  subtype3  87   5   5
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      150       72       87
  M1       11        5        5
  MX        8        4        5
[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"
D8V7, binary
          cls
clus         0   1
  subtype1  67 102
  subtype2  33  48
  subtype3  37  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67  102
  subtype2   33   48
  subtype3   37   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       67       33       37
  MALE        102       48       60
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    33
  subtype2                                    22
  subtype3                                     7
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     77
  subtype2                                                     36
  subtype3                                                     42
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                26
  subtype2                                                                 6
  subtype3                                                                21
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               21
  subtype2                                                6
  subtype3                                               18
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        7
  subtype2                                                        8
  subtype3                                                        5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         0
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        1
  subtype3                                        0
D8V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   33
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  77
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        21
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        18
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1   3 166
  subtype2   1  80
  subtype3   3  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  166
  subtype2    1   80
  subtype3    3   94
     clus
vv    subtype1 subtype2 subtype3
  NO         3        1        3
  YES      166       80       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 133   6   8  15
  subtype2  62   4   1   7
  subtype3  83   3   3   3
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      133       62       83
  R1        6        4        3
  R2        8        1        3
  RX       15        7        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    37                         3   102
  subtype2    20                         1    54
  subtype3    28                         0    52
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           37       20       28
  BLACK OR AFRICAN AMERICAN        3        1        0
  WHITE                          102       54       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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 53 23
  subtype2 97 22
  subtype3 62 32
subtype1 subtype2 subtype3 
      76      119       94 
subtype1 subtype2 subtype3 
      23       22       32 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        5.62        11.70        34.68        15.95        13.12         7.00 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 
        0.62        32.78        16.14         1.25        30.90        32.94 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8291 
        0.16        12.43        12.76        20.55         0.72        16.31 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
        1.48         6.18        19.50         0.26         0.95        19.17 
TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
        0.72        15.81        13.45         5.13         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8531 TCGA-CD-A4MG TCGA-CG-4437 
       13.18         0.30         0.39         0.10         0.07         8.05 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       14.01        19.07         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       20.55        18.84        17.85        13.35        17.19        15.22 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-EQ-5647 
       12.79        24.72        15.16        13.78         9.76         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8608 
        6.58        14.47        21.27        26.47         1.51        10.62 
TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-IN-7808 TCGA-IN-8462 
       10.19        17.69         3.45        18.81 

$subtype2
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 
       24.76        35.24        23.93        15.42         0.69        18.54 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8362 
        1.32         0.69        12.26        12.95         1.55         0.36 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
        4.31         3.32        14.79         0.26        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 
        9.21        20.22         1.12         7.53        11.54        15.81 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        0.62        10.68         1.15         0.66         2.27         0.92 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       12.89         0.72        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 
       11.57         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
        0.10         0.07         0.13         0.13         0.10         0.10 
TCGA-CG-5725 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 
       15.02        10.26        15.98        11.31        12.33        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A6EV TCGA-D7-A6EX 
        0.23         6.97        14.27         5.92        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 
        2.96        15.65         7.40        16.24        72.23        19.53 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        13.58         0.56        11.08         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       18.08         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         6.51         6.25         2.10        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8663 
       12.30         9.67         8.88         8.81        27.42         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       18.38         5.19        13.08         1.41         6.44         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ 
        5.56         1.81         2.53         5.56        60.56         4.50 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       16.67       122.30        37.91         8.94         5.79 

$subtype3
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       10.13        13.68        39.12         0.82        13.84        13.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7716 
        8.98        21.11        31.20        12.82         9.21        28.01 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
        0.95         0.69        18.71        17.49         0.82         0.49 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        0.26         0.26         7.40        22.19         2.96        13.74 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 
       14.04         0.36         0.69         3.72        12.79         2.14 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        0.20         0.49        16.44         0.59        15.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        3.02        13.41        13.51         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       12.82         0.66        19.36        13.51         0.46         2.83 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5717 TCGA-D7-5579 TCGA-D7-6518 
        0.13         0.13         0.10         6.97        11.93        19.13 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 
       18.54        18.61        10.55        16.80        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A748 
       20.91        16.44        14.76        13.71        11.44         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.13         7.79         8.12         0.39         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7806 
       59.54         5.03        21.37         0.10         0.26        21.21 
TCGA-IN-A6RJ TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.36         3.72        11.05         4.67        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-ZA-A8F6 
      116.38        71.38        57.44         4.21 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  105.07   122.30   116.38 
subtype1 subtype2 subtype3 
  12.775    9.210    9.670 
[1] "0.1 - 105.1 (12.8)" "0.1 - 122.3 (9.2)"  "0.1 - 116.4 (9.7)" 
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        1        7       10         9        11         1
  subtype2       1       10       16        7        15        20         0
  subtype3       0        0        9        8         9        15         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         15          9          6        8
  subtype2         25         15         14        3
  subtype3         15         20         11        8
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA          1       10        0
  STAGE IB          7       16        9
  STAGE II         10        7        8
  STAGE IIA         9       15        9
  STAGE IIB        11       20       15
  STAGE III         1        0        1
  STAGE IIIA       15       25       15
  STAGE IIIB        9       15       20
  STAGE IIIC        6       14       11
  STAGE IV          8        3        8
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2 25 33 18
  subtype2 15 30 54 27
  subtype3  1 16 48 31
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2       15        1
  T2       25       30       16
  T3       33       54       48
  T4       18       27       31
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 26 22 17 13
  subtype2 48 29 26 23
  subtype3 29 24 17 25
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       26       48       29
  N1       22       29       24
  N2       17       26       17
  N3       13       23       25
[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  69   7   2
  subtype2 118   1   7
  subtype3  85   6   5
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       69      118       85
  M1        7        1        6
  MX        2        7        5
[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 28 50
  subtype2 50 76
  subtype3 37 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   50
  subtype2   50   76
  subtype3   37   59
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       50       37
  MALE         50       76       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    12
  subtype2                                    11
  subtype3                                    34
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     32
  subtype2                                                     59
  subtype3                                                     35
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                20
  subtype2                                                                15
  subtype3                                                                 9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                9
  subtype2                                               29
  subtype3                                                6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                        5
  subtype3                                                       11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         4
  subtype3                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        2
  subtype3                                        1
D9V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   34
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus         0   1
  subtype1   1  77
  subtype2   5 121
  subtype3   1  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   77
  subtype2    5  121
  subtype3    1   95
     clus
vv    subtype1 subtype2 subtype3
  NO         1        5        1
  YES       77      121       95
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2
  subtype1  66   2   5
  subtype2 114   6   0
  subtype3  84   4   0
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       66      114       84
  R1        2        6        4
  R2        5        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    11                         1    48
  subtype2    44                         2    71
  subtype3    30                         1    64
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           11       44       30
  BLACK OR AFRICAN AMERICAN        1        2        1
  WHITE                           48       71       64
[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 121  37
  subtype2  40  19
  subtype3  51  21
subtype1 subtype2 subtype3 
     158       59       72 
subtype1 subtype2 subtype3 
      37       19       21 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        5.62        11.70        34.68        15.95        13.12         7.00 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 
       32.78        16.14         1.25        30.90        32.94        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 
       35.24        23.93        15.42         0.69        12.43        12.76 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       17.49        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 
       16.31         1.48         6.18        19.50         0.26         0.95 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 
        4.31        19.17         0.26        15.85         0.72        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A44U 
        1.12        15.81        13.45         7.53        15.81         1.15 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4PF 
        2.27         0.92        12.89         0.53        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 
       11.57         5.13         3.25        13.18         0.39         0.10 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
        0.10         0.10         0.10         0.13         0.07         0.10 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        8.05        14.01         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        79.07         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       21.07         7.99        12.36        12.66        20.55        18.54 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        17.19        15.22        12.79        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YX 
       19.50        17.19         0.23         6.97        14.27        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 
       13.78        14.76        11.24         9.76        15.65         4.34 
TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BE 
        8.12         0.39        19.53        17.06        13.58        11.08 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        1.55         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ 
        5.59        12.30        11.84        24.20         3.25        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        19.36        17.69         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU 
        5.19        13.08         1.41         6.44         6.87         1.81 
TCGA-IP-7968 TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
        2.53         3.72        11.05        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N5 
      115.69        57.44 

$subtype2
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       13.68        39.12         0.82        13.84        13.22         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7959 
       21.11        31.20        12.82         0.16         0.69        18.71 
TCGA-BR-8080 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
        0.49        22.19         2.96        13.74        14.04         0.36 
TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
        0.69         3.72        12.79         0.20         0.49        16.44 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       15.68        12.56         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        12.82         0.66        19.36        13.51         0.46 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5719 TCGA-CG-5728 
        2.83         0.07         0.13         0.10         1.02        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET 
       11.93        19.13        18.61        20.91        16.44        13.71 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        7.13         0.62         3.02        22.29        59.54         5.03 
TCGA-HU-A4GQ TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-ZA-A8F6 
        0.10         4.67       116.38        71.38         4.21 

$subtype3
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
       10.13         0.62         9.21        28.01        18.54         0.95 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        0.82         1.32         0.69         0.26         1.55         7.40 
TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8590 
        0.36         3.32        14.79         5.39         9.21         2.14 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 
       11.54         0.59         0.62        10.68         0.66         0.72 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
       20.65        13.64        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.13         0.16         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4449 TCGA-CG-5718 
        0.07         0.13         0.13         0.10        19.07         1.02 
TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       15.02        18.84        10.26        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6EY 
       12.33        16.80        21.14         5.92        11.31        11.44 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD 
        2.96         7.79         0.56        12.59        14.17        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A7NT 
       25.81        11.77        12.95        12.30        27.42         5.56 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        5.56        60.56         4.50        37.91         8.94         5.79 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    60.56 
subtype1 subtype2 subtype3 
  11.935   12.790    6.660 
[1] "0.1 - 122.3 (11.9)" "0.1 - 116.4 (12.8)" "0.1 - 60.6 (6.7)"  
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2       10       17       12        19        25         1
  subtype2       0        0        7        3         8         8         0
  subtype3       0        1        8       10         6        13         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         29         22         19       10
  subtype2          7         14          7        6
  subtype3         19          8          5        3
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        0
  STAGE IA         10        0        1
  STAGE IB         17        7        8
  STAGE II         12        3       10
  STAGE IIA        19        8        6
  STAGE IIB        25        8       13
  STAGE III         1        0        1
  STAGE IIIA       29        7       19
  STAGE IIIB       22       14        8
  STAGE IIIC       19        7        5
  STAGE IV         10        6        3
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 16 44 67 39
  subtype2  0  9 30 21
  subtype3  2 18 38 16
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       16        0        2
  T2       44        9       18
  T3       67       30       38
  T4       39       21       16
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 57 41 35 33
  subtype2 22 11  8 18
  subtype3 24 23 17 10
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       57       22       24
  N1       41       11       23
  N2       35        8       17
  N3       33       18       10
[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 150   7   9
  subtype2  52   5   3
  subtype3  70   2   2
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      150       52       70
  M1        7        5        2
  MX        9        3        2
[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  58 108
  subtype2  26  34
  subtype3  31  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58  108
  subtype2   26   34
  subtype3   31   43
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       58       26       31
  MALE        108       34       43
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    31
  subtype2                                    21
  subtype3                                     5
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     74
  subtype2                                                     22
  subtype3                                                     30
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                23
  subtype2                                                                 5
  subtype3                                                                16
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               25
  subtype2                                                4
  subtype3                                               15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        8
  subtype2                                                        7
  subtype3                                                        4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         0
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        1
  subtype3                                        0
D10V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  74
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus         0   1
  subtype1   4 162
  subtype2   0  60
  subtype3   3  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  162
  subtype2    0   60
  subtype3    3   71
     clus
vv    subtype1 subtype2 subtype3
  NO         4        0        3
  YES      162       60       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2
  subtype1 148   7   4
  subtype2  50   3   1
  subtype3  66   2   0
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      148       50       66
  R1        7        3        2
  R2        4        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    43                         4    99
  subtype2    17                         0    41
  subtype3    25                         0    43
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           43       17       25
  BLACK OR AFRICAN AMERICAN        4        0        0
  WHITE                           99       41       43
[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"
