[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/11541908/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/11724821/STAD-TP.mergedcluster.txt"

nPatients in clinical file=397, in cluster file=443, common to both=397
[1]  10 397
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
108 173  32  64  18 
  1   2   3   4   5 
108 173  32  64  18 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
121  92 106 
  1   2   3 
121  92 106 
[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 
166 125 105 
  1   2   3 
166 125 105 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 73 155  76  92 
  1   2   3   4 
 73 155  76  92 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
62 43 61 49 31 56 
 1  2  3  4  5  6 
62 43 61 49 31 56 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
174  69  59 
  1   2   3 
174  69  59 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "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 397 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          677 
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          193 
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          181 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
         523          126          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-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
          NA          196           NA          209          169           55 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
          77          169         1842          879           NA          600 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
         131           NA           NA           NA           NA         3720 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        1153         1236         3519         3540         2171           NA 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
          NA         1083           NA          176           NA         1148 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
          NA           NA           NA          946           NA          680 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
         723           NA          580         1023           NA           NA 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
          NA           NA           NA           NA           NA           NA 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
         587          717         1964           NA         1800          873 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
          NA          264         1498           NA           NA          224 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
         261           NA         1346          262           NA           NA 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
          NA           NA         1219          912          642          128 
TCGA-ZQ-A9CR 
          NA 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=114,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=231,	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=8,	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=7,	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=33,	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=27,	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 397 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=53, 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 
 21  87 175 104 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 21  87 175 104 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 21  87 175 104 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 21  87 175 104 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
124 107  75  79 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
124 107  75  79 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
124 107  75  79 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
124 107  75  79 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, 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=33, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  67  34
  subtype2 105  56
  subtype3  17  13
  subtype4  42  15
  subtype5  11   4
subtype1 subtype2 subtype3 subtype4 subtype5 
     101      161       30       57       15 
subtype1 subtype2 subtype3 subtype4 subtype5 
      34       56       13       15        4 
$subtype1
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-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PE TCGA-BR-A4QI 
       11.54        10.68         0.66        22.26        20.42        13.64 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 
       13.15         0.30         0.07         0.10         0.13         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.13         0.13         0.10        20.02         3.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        7.99        54.08        29.98        47.05        19.07        21.99 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 
       18.97        22.98        15.02         4.01        55.04        11.93 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.22        15.98        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-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF 
        1.55         5.92        12.59        14.17        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
       11.77         2.10        12.95        12.30        27.42        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.19         1.41         6.74         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DU 
       28.90         8.61         8.94        35.61         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91X 
       13.25        13.02         2.70        17.85         1.71         8.58 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       44.25         8.61         4.54        40.08        29.98 

$subtype2
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-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
       13.74         4.31         0.36        19.17         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       15.85         3.72         1.12        12.79         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
        0.20         0.49        15.81        15.68        12.56         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       12.82        19.36         0.46        11.57         5.13         2.83 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.07         0.13         0.10         0.10         0.10         0.10 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
        1.02         8.05         9.01        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        6.02         0.99       105.07        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.36        18.61        17.85        24.72        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6177 TCGA-F1-6874 
       11.44         9.76         4.34         7.13         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB 
       21.27        22.29        59.54         5.03         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       26.47        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
        5.59        11.84        21.37        29.98         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RJ TCGA-MX-A5UG TCGA-MX-A5UJ 
        0.26         8.88         8.81         5.36         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.31        11.05         4.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8P2 
      116.38        71.38        57.44        16.87         5.79        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM 
       23.77        19.07        33.63        46.26        16.31         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        23.41        15.65        19.30        59.18        11.70 
TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-ZA-A8F6 
       49.25         7.36        55.43         6.58         4.21 

$subtype3
TCGA-B7-5818 TCGA-BR-6801 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8682 
       11.70        21.11         0.36         3.32         5.39        16.44 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-A4MG TCGA-CG-4304 
        0.59         1.15        13.51        13.18         0.07        27.02 
TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        4.01         7.07         1.02        12.03        28.96        79.07 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.66        19.13        18.54        19.50         6.97        21.14 
TCGA-HU-A4G6 TCGA-HU-A4GQ TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8PY TCGA-VQ-AA6J 
       12.30         0.10        37.74        21.73        14.33        21.11 

$subtype4
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-8687 TCGA-BR-A4CS TCGA-BR-A4J1 
       19.50         0.72        15.81         0.62         0.92         0.72 
TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8524 TCGA-CD-8526 
        0.66        20.65         1.15         3.25         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A48C TCGA-CG-4472 
        0.07         0.16         0.10         0.13         0.13        12.00 
TCGA-CG-5719 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-8575 TCGA-D7-A4YU 
        1.02        20.55        18.84         5.95         0.23        16.44 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-HU-8238 
       11.31         7.40         8.12         3.02        17.06         1.51 
TCGA-HU-A4G2 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 
       24.30         6.25        17.69         9.67        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       18.81         3.39        13.08         6.44         5.56         1.81 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PU TCGA-VQ-A8PX 
       16.67       122.30        31.10         7.73        23.57        64.57 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91Y 
       28.70         8.68         9.73 

$subtype5
TCGA-BR-8369 TCGA-BR-8676 TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-D7-6817 
       14.04         7.53        15.95        14.01        12.03        12.79 
TCGA-D7-A6EV TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4H3 TCGA-IN-A6RS 
       11.24        24.20         3.25         8.98        19.36         6.87 
TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-ZQ-A9CR 
       20.81         5.72         0.79 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.07     0.07     0.07     0.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
   72.23   116.38    79.07   122.30    24.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
   11.54    12.26    12.92     7.40    12.03 
[1] "0.1 - 72.2 (11.5)"  "0.1 - 116.4 (12.3)" "0.1 - 79.1 (12.9)" 
[4] "0.1 - 122.3 (7.4)"  "0.8 - 24.2 (12.0)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        5       15        8         9        15         0
  subtype2       1        3       18       12        17        23         2
  subtype3       0        2        3        2         4         1         0
  subtype4       0        1        2        7         5         9         1
  subtype5       1        2        1        2         1         1         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         25         10          5       12
  subtype2         30         26         17       16
  subtype3          5          8          3        3
  subtype4         15          8         10        4
  subtype5          2          3          2        2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        1        0        0        1
  STAGE IA          5        3        2        1        2
  STAGE IB         15       18        3        2        1
  STAGE II          8       12        2        7        2
  STAGE IIA         9       17        4        5        1
  STAGE IIB        15       23        1        9        1
  STAGE III         0        2        0        1        0
  STAGE IIIA       25       30        5       15        2
  STAGE IIIB       10       26        8        8        3
  STAGE IIIC        5       17        3       10        2
  STAGE IV         12       16        3        4        2
[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 28 50 22
  subtype2  7 34 72 55
  subtype3  2  7 17  6
  subtype4  3 11 30 18
  subtype5  3  7  4  3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        7        2        3        3
  T2       28       34        7       11        7
  T3       50       72       17       30        4
  T4       22       55        6       18        3
[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 36 33 19 16
  subtype2 55 48 30 34
  subtype3 11  2  7 11
  subtype4 16 21 16 11
  subtype5  4  3  3  7
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       36       55       11       16        4
  N1       33       48        2       21        3
  N2       19       30        7       16        3
  N3       16       34       11       11        7
[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  94   7   7
  subtype2 153  13   7
  subtype3  30   2   0
  subtype4  59   2   3
  subtype5  17   0   1
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       94      153       30       59       17
  M1        7       13        2        2        0
  MX        7        7        0        3        1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 35 73
  subtype2 77 96
  subtype3  6 26
  subtype4 25 39
  subtype5  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   73
  subtype2   77   96
  subtype3    6   26
  subtype4   25   39
  subtype5    8   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       35       77        6       25        8
  MALE         73       96       26       39       10
[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                                     6
  subtype2                                    38
  subtype3                                     7
  subtype4                                    11
  subtype5                                     3
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     44
  subtype2                                                     71
  subtype3                                                      8
  subtype4                                                     28
  subtype5                                                      6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                23
  subtype2                                                                24
  subtype3                                                                 9
  subtype4                                                                10
  subtype5                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               24
  subtype2                                               19
  subtype3                                                6
  subtype4                                               11
  subtype5                                                4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        4
  subtype2                                                       12
  subtype3                                                        1
  subtype4                                                        3
  subtype5                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         4
  subtype2                                                         2
  subtype3                                                         1
  subtype4                                                         0
  subtype5                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        7
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
D1V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  71
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 7
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  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                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 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   2 106
  subtype2   1 172
  subtype3   0  32
  subtype4   2  62
  subtype5   1  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  106
  subtype2    1  172
  subtype3    0   32
  subtype4    2   62
  subtype5    1   17
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        1        0        2        1
  YES      106      172       32       62       17
[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  84   4   8   5
  subtype2 139   8   7  13
  subtype3  26   2   2   1
  subtype4  52   2   1   5
  subtype5  17   0   0   1
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       84      139       26       52       17
  R1        4        8        2        2        0
  R2        8        7        2        1        0
  RX        5       13        1        5        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    26                         3
  subtype2    34                         2
  subtype3     6                         1
  subtype4    18                         0
  subtype5     4                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    60
  subtype2                                         0   117
  subtype3                                         0    16
  subtype4                                         0    41
  subtype5                                         0     9
D1V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           26       34        6       18
  BLACK OR AFRICAN AMERICAN                        3        2        1        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           60      117       16       41
                                           clus
vv                                          subtype5
  ASIAN                                            4
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                            9
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 94 23
  subtype2 58 30
  subtype3 66 37
subtype1 subtype2 subtype3 
     117       88      103 
subtype1 subtype2 subtype3 
      23       30       37 
$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 
       22.26         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         5.95        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-A6RR TCGA-IN-A6RS TCGA-IN-A7NU 
        3.39         1.41         6.44         6.74         6.87         1.81 
TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.73        16.67        37.74        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        7.73        19.07        33.63 

$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         6.35         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         4.14        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-KB-A93H TCGA-RD-A7BT TCGA-RD-A8N6 
       13.08         5.56         2.53        28.90         8.61         8.94 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-ZQ-A9CR 
        5.46        13.25        13.02         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-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       60.56         3.72         4.31        11.05         4.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8PC 
       35.61        16.87         5.79         0.92        31.10        46.26 
TCGA-ZA-A8F6 
        4.21 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
   65.10    79.07   122.30 
subtype1 subtype2 subtype3 
  12.100   10.435   10.130 
[1] "0.1 - 65.1 (12.1)"  "0.1 - 79.1 (10.4)"  "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        8        15        22         0
  subtype2       0        3       10       10         8        15         0
  subtype3       0        1       11        8        14        10         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         19         19         14        3
  subtype2         20         10          8        8
  subtype3         25         17         10        8
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        0
  STAGE IA          7        3        1
  STAGE IB         12       10       11
  STAGE II          8       10        8
  STAGE IIA        15        8       14
  STAGE IIB        22       15       10
  STAGE III         0        0        2
  STAGE IIIA       19       20       25
  STAGE IIIB       19       10       17
  STAGE IIIC       14        8       10
  STAGE IV          3        8        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 11 24 53 33
  subtype2  4 28 40 20
  subtype3  3 20 55 28
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       11        4        3
  T2       24       28       20
  T3       53       40       55
  T4       33       20       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 47 29 19 26
  subtype2 30 24 20 18
  subtype3 33 28 23 21
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       47       30       33
  N1       29       24       28
  N2       19       20       23
  N3       26       18       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 119   1   1
  subtype2  78   5   9
  subtype3  92   9   5
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      119       78       92
  M1        1        5        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 45 76
  subtype2 34 58
  subtype3 43 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   76
  subtype2   34   58
  subtype3   43   63
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       34       43
  MALE         76       58       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                                    19
  subtype2                                     5
  subtype3                                    35
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     52
  subtype2                                                     39
  subtype3                                                     37
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                17
  subtype2                                                                18
  subtype3                                                                15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               21
  subtype2                                               24
  subtype3                                                5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        8
  subtype2                                                        2
  subtype3                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         3
  subtype2                                                         3
  subtype3                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        1
  subtype3                                        4
D2V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  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)       18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   35
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
[1] 7 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   1 120
  subtype2   4  88
  subtype3   1 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  120
  subtype2    4   88
  subtype3    1  105
     clus
vv    subtype1 subtype2 subtype3
  NO         1        4        1
  YES      120       88      105
[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 111   4   1
  subtype2  76   4   4
  subtype3  93   5   2
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      111       76       93
  R1        4        4        5
  R2        1        4        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                         3
  subtype2    25                         3
  subtype3    29                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    73
  subtype2                                         1    54
  subtype3                                         0    69
D2V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           34       25       29
  BLACK OR AFRICAN AMERICAN                        3        3        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           73       54       69
[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 57 28
  subtype3 53 26
subtype1 subtype2 subtype3 
      70       85       79 
subtype1 subtype2 subtype3 
      19       28       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         5.95        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        22.26         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         6.35         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 
        4.14        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 
   8.515    9.570   12.790 
[1] "0.1 - 105.1 (8.5)" "0.1 - 65.1 (9.6)"  "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        11         1
  subtype2       0        2        3       12        10        14         1
  subtype3       2        4       13       12         5        10         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         15         12          8        6
  subtype2         15         11         11        9
  subtype3         13         11          5        8
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        11       14       10
  STAGE III         1        1        1
  STAGE IIIA       15       15       13
  STAGE IIIB       12       11       11
  STAGE IIIC        8       11        5
  STAGE IV          6        9        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  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 \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                       12
  subtype3                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         3
          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 \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 \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 \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 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  4 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    0   91
  subtype3    4   87
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        4
  YES       80       91       87
[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 52 33
subtype1 subtype2 subtype3 subtype4 
      32       72       45       85 
subtype1 subtype2 subtype3 subtype4 
       6       23       11       33 
$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        22.26        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         6.35         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 
        5.95        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         4.14 
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   12.725   10.620    7.430 
[1] "0.1 - 105.1 (12.3)" "0.1 - 79.1 (12.7)"  "0.1 - 72.2 (10.6)" 
[4] "0.1 - 65.1 (7.4)"  
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        7        4         3         5         0
  subtype2       0        3       10       11         4         8         1
  subtype3       2        2        4        3         7         4         1
  subtype4       0        0        4       10        11        18         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          4          5          3        0
  subtype2         16         10          2       13
  subtype3         11          8          5        3
  subtype4         12         11         14        7
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         5        8        4       18
  STAGE III         0        1        1        1
  STAGE IIIA        4       16       11       12
  STAGE IIIB        5       10        8       11
  STAGE IIIC        3        2        5       14
  STAGE IV          0       13        3        7
[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 \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                                                         1
          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 \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 \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 \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 \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 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  0 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    6   78
  subtype3    0   55
  subtype4    0   91
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        6        0        0
  YES       34       78       55       91
[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 35 23
  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       23       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 
        5.95        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         4.14        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 
        6.35         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 
  12.890    9.850    8.810   13.215    9.210 
[1] "0.1 - 105.1 (12.9)" "0.1 - 59.5 (9.9)"   "0.1 - 55.0 (8.8)"  
[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         10         12         10        5
  subtype3          7          5          3       10
  subtype4          5          3          0        3
  subtype5         12          6          4        4
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       10        7        5       12
  STAGE IIIB        6       12        5        3        6
  STAGE IIIC        6       10        3        0        4
  STAGE IV          3        5       10        3        4
[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 \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                                                         1
  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 \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 \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 \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  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 \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 \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 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  4 42
  subtype4  0 37
  subtype5  2 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    0   63
  subtype3    4   42
  subtype4    0   37
  subtype5    2   60
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         0        0        4        0        2
  YES       66       63       42       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 28 11
  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       11        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         5.95 
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         4.14        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         6.35         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    9.325   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 (9.3)"  "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          8          8          7        3
  subtype4          9          5          4        9
  subtype5          4          3          1        5
  subtype6         13          3          3        0
  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        8        9        4       13        1
  STAGE IIIB        4        6        8        5        3        3        3
  STAGE IIIC        1        2        7        4        1        3        5
  STAGE IV          7        1        3        9        5        0        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 \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                                                         1
  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 \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 \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 \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 \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  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 \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 \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 \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 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  4 58
  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    4   58
  subtype5    0   42
  subtype6    2   38
  subtype7    0   21
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        0        0        4        0        2        0
  YES       38       21       50       58       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 103  44
  subtype2  71  47
  subtype3  70  30
subtype1 subtype2 subtype3 
     147      118      100 
subtype1 subtype2 subtype3 
      44       47       30 
$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-7703 
       32.78        16.14         1.25        30.90        32.94        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8296 
       35.24        23.93        12.26        20.55        12.95         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
        6.18        19.50         0.26         4.31        19.17        15.85 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4CQ 
        0.72        20.22         1.12        15.81        15.81        22.26 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 
       11.57         5.13         3.25        13.18         0.30         0.39 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 
        0.10         0.10         0.13         0.07         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
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-5720 TCGA-CG-5721 
        7.07        22.98        30.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6524 TCGA-D7-6525 
       21.07         7.99        12.36        20.55        17.85         5.95 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8575 
        4.14        15.22        15.98        12.79        24.72         0.23 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6177 
       15.16        13.78         9.76        15.65         7.40         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BE 
       14.47        21.27        19.53        17.06        13.58        11.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G3 
       26.47         1.51        14.27        12.10        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP 
       12.30        11.84        24.20         3.25        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.51         6.25        10.19        17.69         9.67         8.88 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A93H 
        3.45        18.81         3.39         6.44         1.81        28.90 
TCGA-RD-A8MV TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8PB TCGA-VQ-A8PC 
      122.30         0.92        21.73        23.77        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU 
       16.31         1.87         9.27        23.41        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 
       49.25         1.71         7.36         8.58        55.43         6.58 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       40.08        29.98        21.11 

$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-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       31.20        12.82         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
        0.69        12.76        18.71        17.49         0.82         0.49 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 
        0.72         0.26         0.26        16.31         7.40         0.36 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19         2.96         0.95        13.74        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 
        0.36         0.69         3.72         5.39        12.79         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       13.45         0.20         0.49        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        0.62        12.56         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 
        0.46        13.64         2.83         0.07         0.13         0.16 
TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
        0.10         0.13         0.10        12.00         6.97         1.02 
TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       65.10        55.04        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       18.54        18.61        10.55        17.19        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A748 
       16.44        14.76        13.71        11.31        11.44         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.13         0.62         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-MX-A5UG TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
        3.72         4.31        11.05         4.67        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8P8 
      116.38        71.38        57.44        35.61        16.87        19.07 
TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-ZA-A8F6 
       15.65         9.73         5.72         4.21 

$subtype3
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 
        9.21        15.42        28.01        18.54         1.32         0.69 
TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8676 TCGA-BR-8678 
        1.55        14.79         0.26         9.21         7.53        11.54 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68         1.15         0.66         0.92        12.89         0.72 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
       20.65        20.42         1.15        13.15         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.07         0.10         0.13         0.13         6.35 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 
        0.13         0.13         0.10        54.08        19.07        21.99 
TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.97        15.02        17.19        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A6EV TCGA-D7-A6F0 
       19.50         6.97        14.27         5.92        11.24         2.96 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
        7.79        16.24        72.23         0.56         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       18.08         5.92        12.59        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.76        22.75        25.81        11.77         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ 
       19.36        12.30         8.81        27.42        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.74         6.87         5.56 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-RD-A8MW 
        2.53         5.56        60.56        19.73        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91Q 
       31.10        22.36         7.73         2.70        17.85        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-ZQ-A9CR 
       44.25         8.61         4.54         0.79 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    72.23 
subtype1 subtype2 subtype3 
  12.790   10.340    9.915 
[1] "0.1 - 122.3 (12.8)" "0.1 - 116.4 (10.3)" "0.1 - 72.2 (9.9)"  
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        8       17       18        17        19         2
  subtype2       0        0        9        8        12        15         1
  subtype3       0        5       13        6         8        15         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         30         17         11       15
  subtype2         23         22         17       14
  subtype3         24         16          9        7
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        0
  STAGE IA          8        0        5
  STAGE IB         17        9       13
  STAGE II         18        8        6
  STAGE IIA        17       12        8
  STAGE IIB        19       15       15
  STAGE III         2        1        0
  STAGE IIIA       30       23       24
  STAGE IIIB       17       22       16
  STAGE IIIC       11       17        9
  STAGE IV         15       14        7
[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 13 44 72 31
  subtype2  0 21 54 47
  subtype3  8 22 48 26
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       13        0        8
  T2       44       21       22
  T3       72       54       48
  T4       31       47       26
[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 55 50 31 23
  subtype2 35 31 22 34
  subtype3 34 26 22 21
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       55       35       34
  N1       50       31       26
  N2       31       22       22
  N3       23       34       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 148  11   7
  subtype2 111  10   4
  subtype3  95   3   7
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      148      111       95
  M1       11       10        3
  MX        7        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 67 99
  subtype2 47 78
  subtype3 37 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   99
  subtype2   47   78
  subtype3   37   68
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       67       47       37
  MALE         99       78       68
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    20
  subtype2                                    38
  subtype3                                     7
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     68
  subtype2                                                     49
  subtype3                                                     41
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                34
  subtype2                                                                14
  subtype3                                                                20
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               28
  subtype2                                               11
  subtype3                                               25
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        6
  subtype2                                                       10
  subtype3                                                        6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         4
  subtype2                                                         1
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        5
  subtype2                                        1
  subtype3                                        3
D7V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  68
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 5
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
[1] 7 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   3 163
  subtype2   1 124
  subtype3   2 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  163
  subtype2    1  124
  subtype3    2  103
     clus
vv    subtype1 subtype2 subtype3
  NO         3        1        2
  YES      163      124      103
[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 126   6   9  17
  subtype2 103   6   4   6
  subtype3  90   4   4   2
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      126      103       90
  R1        6        6        4
  R2        9        4        4
  RX       17        6        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    29                         3    98
  subtype2    28                         2    88
  subtype3    32                         2    57
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           29       28       32
  BLACK OR AFRICAN AMERICAN        3        2        2
  WHITE                           98       88       57
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 48 17
  subtype2 98 43
  subtype3 44 28
  subtype4 54 33
subtype1 subtype2 subtype3 subtype4 
      65      141       72       87 
subtype1 subtype2 subtype3 subtype4 
      17       43       28       33 
$subtype1
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6458 
        5.62         6.97        30.90         6.61        34.68         7.00 
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 
       32.78        32.94        23.93        12.95         6.18        19.50 
TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4PE 
        4.31         0.72         1.12        15.81         1.15        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A48C 
        1.15        11.57         3.25         0.10         0.10         0.13 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4465 
        0.07         0.10        15.95         7.99        12.03         9.01 
TCGA-CG-4469 TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YY TCGA-D7-A6EV 
        7.07         4.01        21.07        15.22        13.78        11.24 
TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE TCGA-FP-A4BF 
       15.65         6.58        14.47        19.53        11.08         1.55 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       14.27        11.41        24.20        29.98         6.51         6.25 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-A6RO TCGA-IN-A6RP 
       19.36        17.69         8.88         3.45         1.41         6.44 
TCGA-IP-7968 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PB 
        2.53        21.73        22.36        23.77         7.73        33.63 
TCGA-VQ-A8PO TCGA-VQ-A91D TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-AA6B 
        9.27        11.70         1.71         8.58        29.98 

$subtype2
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6453 TCGA-BR-6455 
       11.70         6.61        18.35         6.18        15.95        13.12 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7703 
       16.14         1.25         8.98        21.11        30.90        24.76 
TCGA-BR-7704 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 
       35.24         0.16        12.43        12.76        17.49        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8363 
       20.55         0.72         0.26        16.31         1.48         0.26 
TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8591 
        0.95        19.17        15.85        20.22        15.81        13.45 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         0.49        22.26         0.92        12.89         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8531 
        0.53         0.66         5.13        13.18         0.39         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4441 
        0.10         0.13         3.02        27.02         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
       29.98        47.05        22.98        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5732 
        6.02         0.99       105.07        12.03        28.96        55.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6524 
        7.99        12.36        12.66        20.55        18.54        17.85 
TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
        5.95        12.79        24.72        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EZ TCGA-D7-A748 
        6.97        14.27        15.16        14.76         9.76         4.34 
TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8211 
        7.40        16.24        72.23        21.27         8.12        13.58 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        0.23        26.47         1.51        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ 
       24.30         5.59        12.30        11.84         3.25        21.37 
TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-HU-A4HB 
        8.98        10.19         0.26         2.10         9.67         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A93H TCGA-RD-A7BS TCGA-RD-A8MV 
        6.74         6.87         1.81        28.90        11.05       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8P8 
       40.64       115.69        57.44         0.92        37.74        19.07 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       46.26        16.31         1.87        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E 
       23.57        64.57        14.33        59.18        28.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       49.25        20.81         7.36        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        5.72        40.08        21.11 

$subtype3
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-6803 TCGA-BR-7196 TCGA-BR-7715 TCGA-BR-7717 
       13.84        13.22        31.20        12.82        15.42         0.69 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 
        0.69        18.71         0.49         0.36        22.19         2.96 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8380 TCGA-BR-8384 
       13.74        14.04         3.32         0.36         0.69         3.72 
TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        5.39        12.79         0.20        16.44         0.59        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4J2 TCGA-BR-A4J5 
       12.56         3.02        13.41        13.51        14.17        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 
       19.36        13.51         0.46        13.64         2.83         0.07 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5728 
        0.13         0.13         0.10        12.00         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-A6EX TCGA-D7-A6EY TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-7735 TCGA-FP-7916 
       11.31        11.44         7.13         0.62         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-MX-A5UG TCGA-RD-A7BW 
       22.29        59.54         5.03         0.10         3.72         4.67 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y TCGA-ZA-A8F6 
      116.38        71.38        35.61        16.87         9.73         4.21 

$subtype4
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-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8687 
       14.79         0.26         9.21         2.14        11.54         0.62 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-5802 
       10.68         0.66         0.72        20.65        13.15         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4306 
        0.13         6.35         0.13         0.10        20.02         1.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5718 
       54.08         4.01        19.07        21.99        18.97         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       15.02        79.07        18.84        17.19         4.14        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YV 
       10.55        11.31        12.33        16.80        21.14         5.92 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 
        2.96         7.79        17.06         0.56        18.08         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 
       12.59        14.17        22.75        25.81        11.77        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.30        27.42        18.38         5.56         5.56        60.56 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       19.73         4.31        16.67        37.91         8.94         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        5.46        13.25        13.02        31.10         2.70        17.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-ZQ-A9CR 
       44.25         8.61         0.79 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
   34.68   122.30   116.38    79.07 
subtype1 subtype2 subtype3 subtype4 
   9.270   12.760   11.685    9.210 
[1] "0.1 - 34.7 (9.3)"   "0.1 - 122.3 (12.8)" "0.1 - 116.4 (11.7)"
[4] "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        3       10        6        11         8         2
  subtype2       0        9       10       12        11        20         0
  subtype3       0        0        8        4         9         6         0
  subtype4       0        1       11       10         6        15         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         10          6          4        5
  subtype2         33         25         16       15
  subtype3         15         15          9        7
  subtype4         19          9          8        9
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           2        0        0        0
  STAGE IA          3        9        0        1
  STAGE IB         10       10        8       11
  STAGE II          6       12        4       10
  STAGE IIA        11       11        9        6
  STAGE IIB         8       20        6       15
  STAGE III         2        0        0        1
  STAGE IIIA       10       33       15       19
  STAGE IIIB        6       25       15        9
  STAGE IIIC        4       16        9        8
  STAGE IV          5       15        7        9
[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  8 20 29 13
  subtype2 10 35 65 43
  subtype3  0 12 36 25
  subtype4  3 20 44 23
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        8       10        0        3
  T2       20       35       12       20
  T3       29       65       36       44
  T4       13       43       25       23
[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 30 19 11  9
  subtype2 44 41 33 34
  subtype3 23 20 10 21
  subtype4 27 27 21 14
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       30       44       23       27
  N1       19       41       20       27
  N2       11       33       10       21
  N3        9       34       21       14
[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  65   5   3
  subtype2 142   7   6
  subtype3  67   5   4
  subtype4  80   7   5
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       65      142       67       80
  M1        5        7        5        7
  MX        3        6        4        5
[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"
D8V7, binary
          cls
clus         0   1
  subtype1  32  41
  subtype2  54 101
  subtype3  31  45
  subtype4  34  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   41
  subtype2   54  101
  subtype3   31   45
  subtype4   34   58
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       32       54       31       34
  MALE         41      101       45       58
[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                                     8
  subtype2                                    28
  subtype3                                    23
  subtype4                                     6
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     34
  subtype2                                                     60
  subtype3                                                     31
  subtype4                                                     33
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                15
  subtype2                                                                25
  subtype3                                                                 6
  subtype4                                                                22
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               10
  subtype2                                               26
  subtype3                                                7
  subtype4                                               21
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                        7
  subtype3                                                        7
  subtype4                                                        5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         3
  subtype3                                                         0
  subtype4                                                         4
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        5
  subtype3                                        1
  subtype4                                        1
D8V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  60
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 5
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[1] 7 4
[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   0  73
  subtype2   4 151
  subtype3   0  76
  subtype4   2  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   73
  subtype2    4  151
  subtype3    0   76
  subtype4    2   90
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        4        0        2
  YES       73      151       76       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  55   2   3   8
  subtype2 130   7   7   9
  subtype3  58   4   2   5
  subtype4  76   3   5   3
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       55      130       58       76
  R1        2        7        4        3
  R2        3        7        2        5
  RX        8        9        5        3
[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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    18                         2    43
  subtype2    27                         3    98
  subtype3    20                         1    52
  subtype4    24                         1    50
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                           18       27       20       24
  BLACK OR AFRICAN AMERICAN        2        3        1        1
  WHITE                           43       98       52       50
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 42 18
  subtype2 33 10
  subtype3 37 22
  subtype4 34 11
  subtype5 20 10
  subtype6 31 24
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      60       43       59       45       30       55 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       10       22       11       10       24 
$subtype1
TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8485 
       18.54         1.32         0.69         1.55         4.31         9.21 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CS 
        7.53        11.54        15.81        10.68         0.66         0.92 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8533 
        0.72        20.65        13.64        11.57         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-5725 TCGA-CG-5730 
        0.13         6.35         0.13         0.10        15.02         4.01 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.33        14.27        11.24        11.31         9.76         2.96 
TCGA-D7-A74A TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GF 
        7.40         0.56        11.08         5.92        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-A6RI TCGA-IN-A7NT 
       11.77         6.51        12.95        12.30        18.38         5.56 
TCGA-KB-A6F7 TCGA-RD-A8MW TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       60.56        37.91         5.79         5.46        13.25        31.10 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91D 
       22.36         7.73        33.63         2.70        17.85        11.70 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA6B 
       20.81         1.71         7.36        44.25         8.61        29.98 

$subtype2
TCGA-BR-6453 TCGA-BR-7703 TCGA-BR-A4QM TCGA-CD-A4MG TCGA-CG-5717 TCGA-D7-6521 
       15.95        24.76         5.13         0.07         6.97        18.54 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-F1-A448 TCGA-FP-8211 
        5.92        14.76        11.44        15.65        21.27        13.58 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4GY 
        5.59        11.84         3.25        21.37        10.19         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RJ TCGA-IN-A6RL 
       17.69         9.67         8.88         8.81         5.36         5.19 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-RD-A8MV 
        6.44         1.81         3.72        19.73        16.67       122.30 
TCGA-RD-A8N1 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PT TCGA-VQ-A8PU 
      115.69        46.26        16.31         1.87        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A927 
       64.57        59.18         8.68         8.58         4.54         6.58 
TCGA-VQ-AA6J 
       21.11 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 
        5.62        11.70        34.68        13.12         7.00         0.62 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 
       30.90        32.94         0.72         1.48         6.18         0.26 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        8.05        14.01        19.07         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-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       11.93        20.55        18.84        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
        4.14        15.22        15.98        12.79        11.31        24.72 
TCGA-D7-A4YY TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-HU-A4GN 
       13.78         0.62         6.58        14.47        29.98 

$subtype4
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8058 
       35.24        23.93         0.69        12.43        12.76        17.49 
TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       12.26        12.95        19.50        19.17         0.26        15.85 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-CD-8525 TCGA-CD-8527 
       20.22         1.12        12.79        13.45         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-D7-8575 TCGA-D7-8576 
        0.13         0.10         0.10         0.10         0.23         6.97 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-HU-8238 
       72.23         0.39        19.53        22.29        17.06         1.51 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       11.41        12.10        10.62        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RN TCGA-IP-7968 TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8PO 
        3.39        13.08         2.53         0.92        21.73         9.27 
TCGA-VQ-A91K TCGA-VQ-A924 TCGA-VQ-AA68 
       49.25        55.43        40.08 

$subtype5
TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8373 
       13.84         9.21        15.42         0.82        16.31        14.79 
TCGA-BR-8677 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-CD-8524 
        0.49        22.26        12.89         0.79        12.82         0.07 
TCGA-CD-8530 TCGA-CD-A48C TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 
        0.16         0.13        10.55        16.80        17.19        21.14 
TCGA-D7-A748 TCGA-EQ-8122 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A8N5 
        4.34         7.79         5.56        28.90         4.31        57.44 
TCGA-RD-A8N9 TCGA-VQ-A8P3 TCGA-VQ-A8PP TCGA-VQ-A91A TCGA-VQ-A928 TCGA-ZQ-A9CR 
       35.61        23.77        23.41        28.70         5.72         0.79 

$subtype6
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6803 TCGA-BR-7196 
       10.13        13.68        39.12         0.82        31.20        12.82 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 
        0.95         0.69        18.71         0.49         0.26         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.36        22.19         2.96        14.04         3.32         0.36 
TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8682 
        0.69         3.72         5.39         2.14         0.20        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.59         0.62        12.56         3.02        13.41        13.51 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-A489 
        0.66        19.36        13.51         0.46         2.83         0.13 
TCGA-CD-A4MI TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET 
        0.10        19.13        18.61        20.91        16.44        13.71 
TCGA-D7-A74B TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-RD-A7BS TCGA-RD-A7BW 
        7.13        59.54         5.03         0.10        11.05         4.67 
TCGA-RD-A8N0 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8P8 TCGA-VQ-A8PQ TCGA-VQ-A91Y 
       40.64         8.94        16.87        19.07        15.65         9.73 
TCGA-ZA-A8F6 
        4.21 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.07     0.07     0.07     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   60.56   122.30   105.07    72.23    57.44    59.54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  10.220   11.440   12.660   12.430   12.855    7.400 
[1] "0.1 - 60.6 (10.2)"  "0.1 - 122.3 (11.4)" "0.1 - 105.1 (12.7)"
[4] "0.1 - 72.2 (12.4)"  "0.1 - 57.4 (12.9)"  "0.1 - 59.5 (7.4)"  
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        9        2         7         6         0
  subtype2       0        2        4        2         2         7         0
  subtype3       1        1        7       12         8         5         0
  subtype4       1        2        3        7         5        10         1
  subtype5       0        0        2        4         2         6         1
  subtype6       0        0        4        2         7         7         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         18          9          5        5
  subtype2         10         10          5        1
  subtype3         13          5          2        7
  subtype4          6          5          7        2
  subtype5          8          4          1        3
  subtype6          9         12         10        5
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        0        1        1        0        0
  STAGE IA          1        2        1        2        0        0
  STAGE IB          9        4        7        3        2        4
  STAGE II          2        2       12        7        4        2
  STAGE IIA         7        2        8        5        2        7
  STAGE IIB         6        7        5       10        6        7
  STAGE III         0        0        0        1        1        0
  STAGE IIIA       18       10       13        6        8        9
  STAGE IIIB        9       10        5        5        4       12
  STAGE IIIC        5        5        2        7        1       10
  STAGE IV          5        1        7        2        3        5
[1] 11  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  3 11 34 14
  subtype2  5 10 18 10
  subtype3  2 25 26  8
  subtype4  3  8 22 16
  subtype5  0  6 15 10
  subtype6  0  7 28 21
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        3        5        2        3        0        0
  T2       11       10       25        8        6        7
  T3       34       18       26       22       15       28
  T4       14       10        8       16       10       21
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20 16 14 12
  subtype2  9 11 15  8
  subtype3 23 17 12  9
  subtype4 23 11  7  8
  subtype5  8 12  3  8
  subtype6 15 11 12 17
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       20        9       23       23        8       15
  N1       16       11       17       11       12       11
  N2       14       15       12        7        3       12
  N3       12        8        9        8        8       17
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 58  3  1
  subtype2 42  0  1
  subtype3 55  5  1
  subtype4 42  2  5
  subtype5 28  1  2
  subtype6 50  5  1
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       58       42       55       42       28       50
  M1        3        0        5        2        1        5
  MX        1        1        1        5        2        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 23 39
  subtype2 13 30
  subtype3 22 39
  subtype4 19 30
  subtype5 13 18
  subtype6 23 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   39
  subtype2   13   30
  subtype3   22   39
  subtype4   19   30
  subtype5   13   18
  subtype6   23   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       23       13       22       19       13       23
  MALE         39       30       39       30       18       33
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     1
  subtype2                                    12
  subtype3                                     6
  subtype4                                     6
  subtype5                                     6
  subtype6                                    20
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     24
  subtype2                                                      9
  subtype3                                                     23
  subtype4                                                     25
  subtype5                                                     12
  subtype6                                                     17
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                16
  subtype2                                                                 5
  subtype3                                                                17
  subtype4                                                                 6
  subtype5                                                                 5
  subtype6                                                                 7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               17
  subtype2                                               11
  subtype3                                               10
  subtype4                                                7
  subtype5                                                4
  subtype6                                                6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        2
  subtype3                                                        3
  subtype4                                                        4
  subtype5                                                        3
  subtype6                                                        5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         1
  subtype3                                                         2
  subtype4                                                         0
  subtype5                                                         1
  subtype6                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        3
  subtype3                                        0
  subtype4                                        1
  subtype5                                        0
  subtype6                                        1
D9V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[1] 7 6
[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 61
  subtype2  0 43
  subtype3  1 60
  subtype4  2 47
  subtype5  1 30
  subtype6  0 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   61
  subtype2    0   43
  subtype3    1   60
  subtype4    2   47
  subtype5    1   30
  subtype6    0   56
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         1        0        1        2        1        0
  YES       61       43       60       47       30       56
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 56  1  2
  subtype2 37  3  1
  subtype3 50  3  4
  subtype4 48  0  0
  subtype5 28  1  0
  subtype6 46  4  2
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       56       37       50       48       28       46
  R1        1        3        3        0        1        4
  R2        2        1        4        0        0        2
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    18                         1    36
  subtype2    12                         1    28
  subtype3     7                         1    36
  subtype4    11                         2    32
  subtype5     8                         0    21
  subtype6    12                         1    43
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           18       12        7       11        8
  BLACK OR AFRICAN AMERICAN        1        1        1        2        0
  WHITE                           36       28       36       32       21
                           clus
vv                          subtype6
  ASIAN                           12
  BLACK OR AFRICAN AMERICAN        1
  WHITE                           43
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 107  57
  subtype2  45  24
  subtype3  45  14
subtype1 subtype2 subtype3 
     164       69       59 
subtype1 subtype2 subtype3 
      57       24       14 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 
        5.62        11.70        34.68        13.12        10.13         7.00 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 
        0.62        32.78         1.25         8.98        30.90        32.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42         0.69 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       18.54        12.43         0.95        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        1.32        12.26         0.72        12.95         0.26         1.55 
TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 
        1.48         0.36         0.26         3.32        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        0.26        15.85         5.39         9.21        20.22        12.79 
TCGA-BR-8591 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       13.45        11.54        15.81         0.59         0.62        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4QI 
        0.66        22.26         0.92        12.89         0.72        13.64 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 
        5.13         3.25        13.15        13.18         0.30         0.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
        0.10         0.13         0.13         6.35         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5717 TCGA-CG-5720 
        0.10         8.05        14.01        19.07         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
       55.04        21.07         7.99        12.36        12.66        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       18.54         5.95        17.19        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU 
       24.72        16.80         6.97        21.14        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
        5.92        13.78        14.76        11.31        11.44         2.96 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       15.65         7.79        72.23         0.39        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-A4GC 
       17.06        13.58         0.56         1.51        12.10         3.25 
TCGA-HU-A4GJ TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.37         9.67         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NT 
        3.39         5.36         5.19        13.08         6.44         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-MX-A663 
        1.81         2.53         5.56        60.56        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL 
       11.05       122.30        37.91         8.94         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
        5.46        13.25        31.10        23.77         7.73        19.07 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PZ 
       46.26        16.31         1.87        23.41        15.65        59.18 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       49.25        20.81        44.25         8.61        55.43         6.58 
TCGA-VQ-AA6B TCGA-VQ-AA6J 
       29.98        21.11 

$subtype2
TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       15.95        13.68        39.12         0.82        13.84        13.22 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 
       21.11        31.20        12.82         0.69        18.71         0.49 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 
       16.31         7.40        22.19         2.96        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-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 
       12.56         3.02        13.41        13.51         0.79        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 
        0.66        19.36        13.51         0.46         2.83         0.07 
TCGA-CD-8524 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 
        0.07         0.13         0.10         1.02        65.10        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8579 
       19.13        18.84        18.61        17.85        17.19        20.91 
TCGA-D7-A6ET TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-8209 TCGA-FP-8210 
       13.71         4.34         7.13         0.62        59.54         5.03 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N0 
        0.10         0.26        28.90         3.72         4.67        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91A TCGA-VQ-A91Y 
      115.69        57.44        35.61        16.87        28.70         9.73 
TCGA-VQ-A928 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72         4.21         0.79 

$subtype3
TCGA-BR-6707 TCGA-BR-8077 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 
       16.14         0.69         6.18        19.50         4.31         1.12 
TCGA-BR-8676 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5718 
        7.53        20.65        11.57         0.10         0.07         1.02 
TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       79.07         4.01         4.14        15.22        15.98        11.31 
TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A74A TCGA-F1-6177 TCGA-F1-6874 
        0.23        11.24         9.76         7.40         6.58        14.47 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G3 
       21.27        11.08         5.92        11.41        10.62         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT 
       11.84        22.75        25.81        11.77        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-A6RI 
       10.19        12.95        17.69        12.30         8.88        18.38 
TCGA-RD-A7C1 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.67        21.73        22.36        33.63         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E 
        9.27        19.30        23.57        64.57        11.70         8.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-AA68 
        1.71         7.36         8.58         4.54        40.08 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   115.69    79.07 
subtype1 subtype2 subtype3 
  11.375   12.560   11.310 
[1] "0.1 - 122.3 (11.4)" "0.1 - 115.7 (12.6)" "0.1 - 79.1 (11.3)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        4       17       19        13        25         2
  subtype2       0        0        5        5         9         6         0
  subtype3       1        2        7        5         9        10         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         42         21         16       14
  subtype2         14         14          9        7
  subtype3          8         10          5        2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        0        1
  STAGE IA          4        0        2
  STAGE IB         17        5        7
  STAGE II         19        5        5
  STAGE IIA        13        9        9
  STAGE IIB        25        6       10
  STAGE III         2        0        0
  STAGE IIIA       42       14        8
  STAGE IIIB       21       14       10
  STAGE IIIC       16        9        5
  STAGE IV         14        7        2
[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  8 41 83 42
  subtype2  0 12 35 22
  subtype3  5 14 25 15
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8        0        5
  T2       41       12       14
  T3       83       35       25
  T4       42       22       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       N0 N1 N2 N3
  subtype1 56 47 37 34
  subtype2 18 17 12 21
  subtype3 24 14 14  7
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       56       18       24
  N1       47       17       14
  N2       37       12       14
  N3       34       21        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"
          vv
clus        M0  M1  MX
  subtype1 158   8   8
  subtype2  61   6   2
  subtype3  56   2   1
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      158       61       56
  M1        8        6        2
  MX        8        2        1
[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  60 114
  subtype2  31  38
  subtype3  22  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60  114
  subtype2   31   38
  subtype3   22   37
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       60       31       22
  MALE        114       38       37
[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                                    20
  subtype2                                    25
  subtype3                                     6
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     78
  subtype2                                                     21
  subtype3                                                     11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                34
  subtype2                                                                 6
  subtype3                                                                16
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               29
  subtype2                                                6
  subtype3                                               20
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        8
  subtype2                                                        9
  subtype3                                                        2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         1
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        1
  subtype3                                        1
D10V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  78
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  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                                   25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[1] 7 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   5 169
  subtype2   0  69
  subtype3   0  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  169
  subtype2    0   69
  subtype3    0   59
     clus
vv    subtype1 subtype2 subtype3
  NO         5        0        0
  YES      169       69       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        R0  R1  R2
  subtype1 155   6   4
  subtype2  56   6   2
  subtype3  54   0   3
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      155       56       54
  R1        6        6        0
  R2        4        2        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    32                         4   113
  subtype2    18                         0    49
  subtype3    18                         2    34
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           32       18       18
  BLACK OR AFRICAN AMERICAN        4        0        2
  WHITE                          113       49       34
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
