
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD-TP/3144511/1.GDAC_mergedClustering.Finished/STAD-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/3132759/1.GDAC_clinicalDataPicker.Finished/STAD-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=181, in cluster file=308, common to both=181
[1]   6 181
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
80 17 12 71 
 1  2  3  4 
80 17 12 71 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
18 30 39 46 
 1  2  3  4 
18 30 39 46 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
28 29 22 29 39 
 1  2  3  4  5 
28 29 22 29 39 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
46 59 42 
 1  2  3 
46 59 42 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
81 39 47 
 1  2  3 
81 39 47 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
38 42 87 
 1  2  3 
38 42 87 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "PATHOLOGICSPREAD(PT)"                  
[11] "PATHOLOGICSPREAD(PN)"                  
[12] "PATHOLOGICSPREAD(M)"                   
[13] "TUMORSTAGE"                            
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "COMPLETENESS.OF.RESECTION"             
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 181 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171            3           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           29           NA           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
          43           NA           41           41           26           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19           19           52           66           30           37 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
          20           34           23           20            8           37 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
          45           14           38            4           32           25 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          138           30           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
           5           33           25           40           21           29 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
          15           14           22            8           13            8 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
          36           47           45           23            6           18 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
          28           12           24           NA           24           16 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
          13            4            7            3           22           15 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
          68           25           21           11           15            9 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
           2           NA           12          609           92          822 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
         485           31         1611          245         1644          122 
TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
         426           NA          912         1431          580          366 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
         669           31          273          576          215          365 
TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
          31           NA           NA           31           31          211 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
          31           31           30          182           29         2131 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
         366          457          881          944         1980          122 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        1674          641          243          263          109          138 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
         298          476          293          249          210           21 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
         181          201          126           51          111          143 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
         123           89          130           19          237          199 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
          61           NA           12            6           92          109 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-7131 TCGA-HF-7132 
          31           NA           NA           17           NA           NA 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
          NA           NA           NA           NA          209          108 
TCGA-IP-7968 
          77 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.T':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "PATHOLOGY.T"                           
 [5] "PATHOLOGY.N"                           
 [6] "PATHOLOGICSPREAD(M)"                   
 [7] "TUMOR.STAGE"                           
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
24 38 39 26 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 181 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 52 57 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 52 57 18 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 52 57 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 52 57 18 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
45 49 23 15 
[1] "table(vv)"
vv
N0 N1 N2 N3 
45 49 23 15 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
45 49 23 15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
45 49 23 15 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 24  38  39  26 
[1] "table(vv)"
vv
  I  II III  IV 
 24  38  39  26 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 24  38  39  26 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 24  38  39  26 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 56  8
  subtype2 11  3
  subtype3  6  2
  subtype4 51  6
subtype1 subtype2 subtype3 subtype4 
      64       14        8       57 
subtype1 subtype2 subtype3 subtype4 
       8        3        2        6 
$subtype1
TCGA-B7-5816 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
        5.62         1.35         0.85         0.82         0.62         1.71 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        2.17         1.22         0.66         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
        1.22         0.46         0.13         0.16         0.99         0.69 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.16         0.82         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.26         1.18         1.48         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5803 TCGA-CG-4306 TCGA-CG-4462 
        0.10         2.24         0.82         0.07         1.02         1.02 
TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        8.98         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5734 
        0.99         5.98         0.95        70.06        65.10         7.99 
TCGA-D7-5577 TCGA-D7-6522 TCGA-D7-6524 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7916 
        8.65         6.90         0.69         6.54         2.01         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 
        3.58        59.05         5.03        26.43 

$subtype2
TCGA-B7-5818 TCGA-BR-6801 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CG-4304 TCGA-CG-4305 
        0.10         1.12         0.23         0.49        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-5726 TCGA-CG-5727 TCGA-D7-5578 
       52.96         4.01         7.07        28.96        31.04         3.58 
TCGA-D7-6518 TCGA-D7-6521 
        9.80         8.19 

$subtype3
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-8297 TCGA-CG-4441 
        0.95         1.41         0.99         1.25         0.76        14.01 
TCGA-CG-4455 TCGA-CG-5733 
       12.03        21.07 

$subtype4
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        1.35         0.62         1.48         1.05         0.82         0.69 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 
        4.54         0.95         1.08         1.32         0.69         0.43 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        0.26         1.55         0.72         0.72         0.49         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 
        0.36         0.30        20.02         3.02         8.05        54.05 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4472 
       29.98        47.05        19.07        21.99        18.94        12.00 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 
        1.02        12.03        15.02         4.01        55.04         4.54 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       15.65         9.63         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
        7.79        72.23         0.39         0.20         1.02         0.56 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.76     0.20 
subtype1 subtype2 subtype3 subtype4 
   70.06    52.96    21.07    72.23 
subtype1 subtype2 subtype3 subtype4 
    0.97     7.63     1.33     3.02 
[1] "0.1 - 70.1 (1.0)" "0.1 - 53.0 (7.6)" "0.8 - 21.1 (1.3)" "0.2 - 72.2 (3.0)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype1" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype1"
 [25] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype1"
 [31] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype4"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [61] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype4" "subtype4" "subtype2"
[103] "subtype2" "subtype1" "subtype4" "subtype4" "subtype3" "subtype1"
[109] "subtype1" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[115] "subtype2" "subtype1" "subtype1" "subtype4" "subtype4" "subtype4"
[121] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[127] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
[133] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[139] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype1" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype1"
 [25] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype1"
 [31] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype4"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [61] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype4" "subtype4" "subtype2"
[103] "subtype2" "subtype1" "subtype4" "subtype4" "subtype3" "subtype1"
[109] "subtype1" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[115] "subtype2" "subtype1" "subtype1" "subtype4" "subtype4" "subtype4"
[121] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[127] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
[133] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[139] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype1" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype1"
 [25] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype1"
 [31] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype4"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [61] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype4" "subtype4" "subtype2"
[103] "subtype2" "subtype1" "subtype4" "subtype4" "subtype3" "subtype1"
[109] "subtype1" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[115] "subtype2" "subtype1" "subtype1" "subtype4" "subtype4" "subtype4"
[121] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[127] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype4"
[133] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[139] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 41 39
  subtype2  3 14
  subtype3  7  5
  subtype4 21 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   39
  subtype2    3   14
  subtype3    7    5
  subtype4   21   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       41        3        7       21
  MALE         39       14        5       50
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     9
  subtype2                                     0
  subtype3                                     1
  subtype4                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      8
  subtype2                                                      1
  subtype3                                                      0
  subtype4                                                      7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 4
  subtype2                                                                 0
  subtype3                                                                 0
  subtype4                                                                 4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        0
  subtype3                                                        0
  subtype4                                                        1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        0
  subtype3                                        0
  subtype4                                        0
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     6
  subtype2                                     4
  subtype3                                     0
  subtype4                                     6
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     34
  subtype2                                                      5
  subtype3                                                      7
  subtype4                                                     27
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 0
  subtype3                                                 1
  subtype4                                                 4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  0
  subtype3                                                  0
  subtype4                                                  2
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                1
  subtype2                                                1
  subtype3                                                0
  subtype4                                                8
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                     10
  subtype2                                                                      6
  subtype3                                                                      3
  subtype4                                                                      9
D1V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  2 17 23  9
  subtype2  2  7  5  2
  subtype3  1  3  6  0
  subtype4  1 25 22  7
D1V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 19 20  9  4
  subtype2  7  2  2  4
  subtype3  3  4  2  0
  subtype4 15 23 10  7
D1V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 43  9  4
  subtype2 15  1  0
  subtype3 11  0  0
  subtype4 49  6  4
D1V7, multiclass
          vv
clus        I II III IV
  subtype1 10 13  15 11
  subtype2  5  3   4  3
  subtype3  0  4   5  0
  subtype4  9 17  15 12
D1V8, multiclass
D1V9, binary
          cls
clus        0  1
  subtype1  1 79
  subtype2  0 17
  subtype3  0 12
  subtype4  4 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   79
  subtype2    0   17
  subtype3    0   12
  subtype4    4   67
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        0        4
  YES       79       17       12       67
          vv
clus       R0 R1 R2 RX
  subtype1 55  2  6 13
  subtype2 12  2  1  1
  subtype3  8  0  0  4
  subtype4 50  3  5  7
D1V10, multiclass
D1V11, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 18  0
  subtype2 24  4
  subtype3 32  5
  subtype4 36  5
subtype1 subtype2 subtype3 subtype4 
      18       28       37       41 
subtype1 subtype2 subtype3 subtype4 
       0        4        5        5 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6852 
        5.62         0.10         1.41         2.17         0.99         0.26 
TCGA-BR-7196 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-A4IY 
        1.22         0.16         0.95         0.46         0.26         0.39 
TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CG-5722 TCGA-D7-5577 TCGA-FP-7916 TCGA-FP-7998 
        0.53         0.49         0.95         8.65         3.02         3.58 

$subtype2
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
        0.95         1.35         0.62         0.46         0.13         0.69 
TCGA-BR-7851 TCGA-BR-7959 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8297 TCGA-BR-A4J8 
        0.99         1.08         0.72         0.43         0.76         0.23 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CG-4437 TCGA-CG-5720 TCGA-CG-5724 
        0.72         0.49         2.24         8.05         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6822 
       28.96        65.10        21.07         5.95         1.68         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-8099 
        6.54         2.01         0.20         1.02 

$subtype3
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 
        1.35         0.85         0.82         1.71         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8291 
        0.76         0.66         0.69         0.82         0.49         1.18 
TCGA-BR-8296 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48         0.20         0.59         0.92         0.79         0.79 
TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 TCGA-CG-5716 TCGA-CG-5717 
        0.43         0.10         0.82         0.07         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 
        1.02         5.98        70.06         7.99         4.54         9.80 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 
        8.19         6.90         0.69        59.05         5.03        26.43 
TCGA-IN-7808 
        3.55 

$subtype4
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        0.62         1.12         1.48         1.25         1.05         0.82 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
        0.16         4.54         0.95         1.32         0.69         0.26 
TCGA-BR-8295 TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.55         0.72         0.13         0.69         0.36         0.30 
TCGA-CD-5813 TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
        0.39        14.01         1.02        15.02        31.04         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
       55.04         3.58        15.65         9.63         6.61         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 
        3.65         4.70         4.04         2.93         0.62         7.79 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8631 TCGA-IN-7806 TCGA-IP-7968 
       72.23         0.39         0.56         6.87         2.53 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.07     0.13 
subtype1 subtype2 subtype3 subtype4 
    8.65    65.10    70.06    72.23 
subtype1 subtype2 subtype3 subtype4 
   0.950    1.005    1.020    1.480 
[1] "0.1 - 8.7 (0.9)"  "0.1 - 65.1 (1.0)" "0.1 - 70.1 (1.0)" "0.1 - 72.2 (1.5)"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype2"
 [25] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [31] "subtype4" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
 [37] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [43] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype4" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [67] "subtype1" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
 [73] "subtype3" "subtype3" "subtype4" "subtype3" "subtype2" "subtype3"
 [79] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype4" "subtype2" "subtype3" "subtype1"
 [91] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype2"
[103] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[109] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[115] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype4"
[121] "subtype3" "subtype4" "subtype3" "subtype4"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype2"
 [25] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [31] "subtype4" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
 [37] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [43] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype4" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [67] "subtype1" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
 [73] "subtype3" "subtype3" "subtype4" "subtype3" "subtype2" "subtype3"
 [79] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype4" "subtype2" "subtype3" "subtype1"
 [91] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype2"
[103] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[109] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[115] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype4"
[121] "subtype3" "subtype4" "subtype3" "subtype4"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype2"
 [25] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [31] "subtype4" "subtype3" "subtype1" "subtype2" "subtype3" "subtype4"
 [37] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [43] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype4" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [67] "subtype1" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
 [73] "subtype3" "subtype3" "subtype4" "subtype3" "subtype2" "subtype3"
 [79] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype4" "subtype2" "subtype3" "subtype1"
 [91] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype2"
[103] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[109] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[115] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype4"
[121] "subtype3" "subtype4" "subtype3" "subtype4"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  7 11
  subtype2 11 19
  subtype3 15 24
  subtype4 17 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   11
  subtype2   11   19
  subtype3   15   24
  subtype4   17   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       11       15       17
  MALE         11       19       24       29
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     1
  subtype2                                     1
  subtype3                                     8
  subtype4                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      5
  subtype2                                                      6
  subtype3                                                      1
  subtype4                                                      4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 1
  subtype2                                                                 1
  subtype3                                                                 2
  subtype4                                                                 4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        1
  subtype3                                                        2
  subtype4                                                        0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
  subtype4                                        0
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     3
  subtype2                                     2
  subtype3                                     6
  subtype4                                     3
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      6
  subtype2                                                      7
  subtype3                                                     13
  subtype4                                                     18
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 0
  subtype2                                                 2
  subtype3                                                 2
  subtype4                                                 2
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  0
  subtype2                                                  1
  subtype3                                                  0
  subtype4                                                  2
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                1
  subtype2                                                2
  subtype3                                                0
  subtype4                                                6
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      1
  subtype2                                                                      7
  subtype3                                                                      4
  subtype4                                                                      7
D2V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  2  7  2
  subtype2  4 10  6  1
  subtype3  0  8 14  3
  subtype4  0 17 18  3
D2V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  4  3  2  2
  subtype2 12  6  2  1
  subtype3  8  9  6  2
  subtype4 13 13  7  5
D2V6, multiclass
          vv
clus       M0 M1 MX
  subtype1  8  2  1
  subtype2 19  1  1
  subtype3 21  4  0
  subtype4 33  2  3
D2V7, multiclass
          vv
clus        I II III IV
  subtype1  1  2   6  2
  subtype2 10  6   3  2
  subtype3  2 10   8  5
  subtype4  4 15  13  6
D2V8, multiclass
D2V9, binary
          cls
clus        0  1
  subtype1  0 18
  subtype2  1 29
  subtype3  0 39
  subtype4  4 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   18
  subtype2    1   29
  subtype3    0   39
  subtype4    4   42
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        0        4
  YES       18       29       39       42
          vv
clus       R0 R1 R2
  subtype1 15  0  1
  subtype2 29  0  1
  subtype3 30  4  1
  subtype4 36  2  2
D2V10, multiclass
D2V11, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 18  2
  subtype2 21  2
  subtype3 13  2
  subtype4 18  5
  subtype5 28  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       23       15       23       32 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        2        2        5        4 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 
        5.62         0.10         0.95         0.99         0.76         0.26 
TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8286 TCGA-CD-5801 TCGA-CG-4305 
        0.13         0.16         0.95         0.43         0.49        15.95 
TCGA-CG-4306 TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-5577 
        1.02         1.02         5.98        70.06        12.03         8.65 
TCGA-D7-6525 TCGA-FP-8099 
        5.95         1.02 

$subtype2
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
        1.41         1.35         0.85         0.82         1.71         2.17 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-8080 TCGA-BR-8284 
        1.12         0.66         1.22         0.69         0.49         0.72 
TCGA-BR-8291 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5813 TCGA-CG-4472 
        1.18         0.76         0.82         0.07         0.39        12.00 
TCGA-D7-6518 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        9.80         3.02         3.58        59.05         5.03 

$subtype3
TCGA-BR-6710 TCGA-BR-7722 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-5716 
        0.66         0.16         3.02         8.05         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-6521 
        6.94         1.02         0.95        55.04         7.99         8.19 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 
        0.69         4.14         4.70 

$subtype4
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8081 TCGA-CD-5799 
        0.62         0.62         0.46         0.99         0.46         0.69 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4469 
       27.02        52.96        14.01        47.05         8.98         7.07 
TCGA-CG-4474 TCGA-CG-5720 TCGA-CG-5726 TCGA-D7-5578 TCGA-D7-6522 TCGA-D7-6528 
        1.02         0.99        28.96         3.58         6.90         1.68 
TCGA-D7-6815 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-IN-7806 
        3.65         6.54         2.01         0.20         6.87 

$subtype5
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        1.35         1.22         1.48         1.05         0.82         0.69 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
        4.54         0.95         1.08         1.32         0.69         0.26 
TCGA-CD-5800 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        0.36        54.05         4.01        29.98        19.07        21.99 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 
       18.94         1.02        15.02        15.65         9.63         6.61 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
        4.04         2.93         4.27         7.79        72.23         0.39 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.07     0.16     0.20     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   70.06    59.05    55.04    52.96    72.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
   1.005    1.180    3.020    3.580    3.240 
[1] "0.1 - 70.1 (1.0)" "0.1 - 59.0 (1.2)" "0.2 - 55.0 (3.0)" "0.2 - 53.0 (3.6)"
[5] "0.3 - 72.2 (3.2)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype5"
  [7] "subtype2" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [13] "subtype1" "subtype5" "subtype3" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype5" "subtype4" "subtype1" "subtype5"
 [25] "subtype5" "subtype5" "subtype3" "subtype5" "subtype4" "subtype5"
 [31] "subtype2" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
 [37] "subtype2" "subtype4" "subtype2" "subtype1" "subtype5" "subtype2"
 [43] "subtype2" "subtype2" "subtype4" "subtype5" "subtype1" "subtype2"
 [49] "subtype2" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype3" "subtype5" "subtype5" "subtype4" "subtype5" "subtype4"
 [61] "subtype5" "subtype5" "subtype3" "subtype4" "subtype5" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype3" "subtype3" "subtype5"
 [73] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype1"
 [79] "subtype5" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype2" "subtype5" "subtype5" "subtype3" "subtype4" "subtype3"
 [91] "subtype1" "subtype5" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype5" "subtype5" "subtype5" "subtype5" "subtype4" "subtype4"
[103] "subtype5" "subtype5" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype2" "subtype2" "subtype4" "subtype5" "subtype5"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype5"
  [7] "subtype2" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [13] "subtype1" "subtype5" "subtype3" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype5" "subtype4" "subtype1" "subtype5"
 [25] "subtype5" "subtype5" "subtype3" "subtype5" "subtype4" "subtype5"
 [31] "subtype2" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
 [37] "subtype2" "subtype4" "subtype2" "subtype1" "subtype5" "subtype2"
 [43] "subtype2" "subtype2" "subtype4" "subtype5" "subtype1" "subtype2"
 [49] "subtype2" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype3" "subtype5" "subtype5" "subtype4" "subtype5" "subtype4"
 [61] "subtype5" "subtype5" "subtype3" "subtype4" "subtype5" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype3" "subtype3" "subtype5"
 [73] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype1"
 [79] "subtype5" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype2" "subtype5" "subtype5" "subtype3" "subtype4" "subtype3"
 [91] "subtype1" "subtype5" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype5" "subtype5" "subtype5" "subtype5" "subtype4" "subtype4"
[103] "subtype5" "subtype5" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype2" "subtype2" "subtype4" "subtype5" "subtype5"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype5"
  [7] "subtype2" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [13] "subtype1" "subtype5" "subtype3" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype5" "subtype4" "subtype1" "subtype5"
 [25] "subtype5" "subtype5" "subtype3" "subtype5" "subtype4" "subtype5"
 [31] "subtype2" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
 [37] "subtype2" "subtype4" "subtype2" "subtype1" "subtype5" "subtype2"
 [43] "subtype2" "subtype2" "subtype4" "subtype5" "subtype1" "subtype2"
 [49] "subtype2" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype3" "subtype5" "subtype5" "subtype4" "subtype5" "subtype4"
 [61] "subtype5" "subtype5" "subtype3" "subtype4" "subtype5" "subtype4"
 [67] "subtype2" "subtype4" "subtype1" "subtype3" "subtype3" "subtype5"
 [73] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype1"
 [79] "subtype5" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype2" "subtype5" "subtype5" "subtype3" "subtype4" "subtype3"
 [91] "subtype1" "subtype5" "subtype3" "subtype4" "subtype4" "subtype3"
 [97] "subtype5" "subtype5" "subtype5" "subtype5" "subtype4" "subtype4"
[103] "subtype5" "subtype5" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype2" "subtype2" "subtype4" "subtype5" "subtype5"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 13 15
  subtype2 11 18
  subtype3  6 16
  subtype4 10 19
  subtype5 13 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   15
  subtype2   11   18
  subtype3    6   16
  subtype4   10   19
  subtype5   13   26
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     0
  subtype2                                     5
  subtype3                                     0
  subtype4                                     0
  subtype5                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      4
  subtype2                                                      0
  subtype3                                                      0
  subtype4                                                      1
  subtype5                                                      1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 0
  subtype2                                                                 1
  subtype3                                                                 0
  subtype4                                                                 0
  subtype5                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        1
  subtype3                                                        0
  subtype4                                                        0
  subtype5                                                        1
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     4
  subtype2                                     3
  subtype3                                     3
  subtype4                                     3
  subtype5                                     3
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     16
  subtype2                                                     15
  subtype3                                                      9
  subtype4                                                     10
  subtype5                                                     17
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 0
  subtype2                                                 2
  subtype3                                                 2
  subtype4                                                 1
  subtype5                                                 1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  1
  subtype4                                                  1
  subtype5                                                  1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                1
  subtype2                                                0
  subtype3                                                1
  subtype4                                                3
  subtype5                                                5
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      3
  subtype2                                                                      1
  subtype3                                                                      5
  subtype4                                                                      8
  subtype5                                                                      6
D3V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  9  9  2
  subtype2  0  2 14  4
  subtype3  0 12  5  4
  subtype4  5 13  7  3
  subtype5  1 12 15  4
D3V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  8  8  2  2
  subtype2  6  9  4  2
  subtype3  4 10  3  5
  subtype4 13  6  5  2
  subtype5 10 11  6  3
D3V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 21  2  1
  subtype2 19  2  1
  subtype3 16  5  1
  subtype4 25  2  1
  subtype5 28  3  3
D3V7, multiclass
          vv
clus        I II III IV
  subtype1  4  5   6  3
  subtype2  0  7   8  5
  subtype3  3  5   6  7
  subtype4 10  6   7  3
  subtype5  6 10   8  6
D3V8, multiclass
D3V9, binary
          cls
clus        0  1
  subtype1  0 28
  subtype2  0 29
  subtype3  4 18
  subtype4  0 29
  subtype5  1 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   28
  subtype2    0   29
  subtype3    4   18
  subtype4    0   29
  subtype5    1   38
          vv
clus       R0 R1 R2 RX
  subtype1 18  0  2  7
  subtype2 18  1  0  5
  subtype3 14  2  4  2
  subtype4 21  1  2  4
  subtype5 27  2  2  4
D3V10, multiclass
D3V11, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 34  2
  subtype2 34  8
  subtype3 30  5
subtype1 subtype2 subtype3 
      36       42       35 
subtype1 subtype2 subtype3 
       2        8        5 
$subtype1
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 
        0.10         1.41         1.35         0.85         0.82         1.71 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7722 
        2.17         0.99         1.12         0.66         1.22         0.16 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
        0.69         0.16         1.08         0.49         0.72         1.18 
TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5813 TCGA-CG-4462 
        0.76         0.82         0.49         0.07         0.39         1.02 
TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5722 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 
       12.00         1.02         0.95         8.65         9.80         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        6.90         0.69         3.02         3.58        59.05         5.03 

$subtype2
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 
        0.95         0.62         0.66         0.76         0.26         0.46 
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 TCGA-CD-5799 
        0.13         0.99         0.95         0.46         0.43         0.69 
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        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4466 
       54.05         4.01        14.01        47.05         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5726 
        7.07         1.02         1.02         1.02         0.99        28.96 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       55.04         7.99         3.58         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6820 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        4.70         2.93         6.54         2.01         0.39         0.20 

$subtype3
TCGA-B7-5816 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 
        5.62         1.35         0.62         1.22         1.48         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
        0.82         0.69         4.54         0.95         1.32         0.69 
TCGA-BR-8289 TCGA-CD-5800 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4477 
        0.26         0.36        29.98        19.07        21.99         1.02 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6519 
        6.94         5.98        70.06        12.03        15.02        15.65 
TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 
        9.63         5.95         6.61         4.04         4.27         7.79 
TCGA-F1-6875 TCGA-FP-8099 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       72.23         1.02         6.87         3.55         2.53 

subtype1 subtype2 subtype3 
    0.07     0.13     0.26 
subtype1 subtype2 subtype3 
   59.05    55.04    72.23 
subtype1 subtype2 subtype3 
    1.02     2.47     4.27 
[1] "0.1 - 59.0 (1.0)" "0.1 - 55.0 (2.5)" "0.3 - 72.2 (4.3)"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [43] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 18 28
  subtype2 22 37
  subtype3 13 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   28
  subtype2   22   37
  subtype3   13   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       22       13
  MALE         28       37       29
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     5
  subtype2                                     0
  subtype3                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      1
  subtype2                                                      3
  subtype3                                                      2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 1
  subtype2                                                                 0
  subtype3                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        0
  subtype3                                                        0
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     7
  subtype2                                     2
  subtype3                                     7
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     22
  subtype2                                                     26
  subtype3                                                     19
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 3
  subtype3                                                 1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  0
  subtype2                                                  2
  subtype3                                                  1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                1
  subtype2                                                5
  subtype3                                                4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      3
  subtype2                                                                     16
  subtype3                                                                      4
D4V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  9 20  5
  subtype2  5 27 12  7
  subtype3  1 12 18  5
D4V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 10 14  6  4
  subtype2 21 16  8  7
  subtype3 10 14  6  3
D4V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 31  5  1
  subtype2 47  6  3
  subtype3 31  3  3
D4V7, multiclass
          vv
clus        I II III IV
  subtype1  2 10  13  8
  subtype2 16 13  10 10
  subtype3  5 10  12  6
D4V8, multiclass
D4V9, binary
          cls
clus        0  1
  subtype1  0 46
  subtype2  4 55
  subtype3  1 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   46
  subtype2    4   55
  subtype3    1   41
     clus
vv    subtype1 subtype2 subtype3
  NO         0        4        1
  YES       46       55       41
          vv
clus       R0 R1 R2 RX
  subtype1 28  2  2  8
  subtype2 40  2  6 10
  subtype3 30  2  2  4
D4V10, multiclass
D4V11, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 49 11
  subtype2 29  3
  subtype3 34  4
subtype1 subtype2 subtype3 
      60       32       38 
subtype1 subtype2 subtype3 
      11        3        4 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 
        5.62         0.10         0.95         1.41         1.35         0.62 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8285 
        0.62         0.99         1.22         0.76         0.26         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 
        1.18         1.48         0.69         0.49         0.30         0.39 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        47.05        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         8.98         7.07         1.02         1.02         1.02 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        28.96        31.04        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        7.99         8.65        15.65         0.69         5.95         6.61 
TCGA-D7-6528 TCGA-D7-6817 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-IN-7808 
        1.68         4.70         0.62         6.54         2.01         3.55 

$subtype2
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
        1.35         0.85         0.82         1.71         2.17         0.66 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7959 
        1.12         0.66         1.22         0.16         0.69         1.08 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8592 TCGA-CD-5798 
        0.82         0.49         0.72         0.76         0.20         0.82 
TCGA-CD-5803 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 
        0.07        12.00         6.94        55.04         4.54         9.80 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-FP-7916 TCGA-FP-7998 
        9.63         8.19         6.90         4.04         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 
       59.05         5.03 

$subtype3
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 
        0.69         4.54         0.99         0.95         0.16         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        0.69         0.95         0.46         0.43         0.26         1.55 
TCGA-CD-5800 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 
        0.36        54.05        19.07        21.99        18.94        15.02 
TCGA-D7-5578 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 
        3.58         4.14         3.65         2.93         4.27         7.79 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 
       72.23         0.39         0.20         1.02         0.56        26.43 
TCGA-IN-7806 TCGA-IP-7968 
        6.87         2.53 

subtype1 subtype2 subtype3 
    0.10     0.07     0.13 
subtype1 subtype2 subtype3 
   70.06    59.05    72.23 
subtype1 subtype2 subtype3 
   2.515    1.285    1.285 
[1] "0.1 - 70.1 (2.5)" "0.1 - 59.0 (1.3)" "0.1 - 72.2 (1.3)"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype3" "subtype1" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 37 44
  subtype2 13 26
  subtype3 16 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   44
  subtype2   13   26
  subtype3   16   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37       13       16
  MALE         44       26       31
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     1
  subtype2                                     5
  subtype3                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      0
  subtype2                                                      0
  subtype3                                                      7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 2
  subtype2                                                                 2
  subtype3                                                                 4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        2
  subtype3                                                        0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     8
  subtype2                                     7
  subtype3                                     1
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     39
  subtype2                                                     17
  subtype3                                                     17
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 2
  subtype3                                                 4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  3
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                5
  subtype2                                                1
  subtype3                                                4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                     20
  subtype2                                                                      2
  subtype3                                                                      6
D5V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  4 30 29 10
  subtype2  0  9 14  4
  subtype3  2 13 14  4
D5V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 24 26 12  9
  subtype2  7 11  6  5
  subtype3 14 12  5  1
D5V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 62 13  3
  subtype2 27  2  1
  subtype3 30  1  4
D5V7, multiclass
          vv
clus        I II III IV
  subtype1 13 19  21 15
  subtype2  2  8  11  6
  subtype3  9 11   7  5
D5V8, multiclass
D5V9, binary
          cls
clus        0  1
  subtype1  0 81
  subtype2  1 38
  subtype3  4 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   81
  subtype2    1   38
  subtype3    4   43
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        4
  YES       81       38       43
          vv
clus       R0 R1 R2 RX
  subtype1 45  3 11 17
  subtype2 28  2  0  5
  subtype3 38  2  1  3
D5V10, multiclass
D5V11, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 29  3
  subtype2 28  3
  subtype3 55 12
subtype1 subtype2 subtype3 
      32       31       67 
subtype1 subtype2 subtype3 
       3        3       12 
$subtype1
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8059 
        0.62         1.48         0.82         4.54         0.95         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-CD-5800 TCGA-CD-5802 
        1.32         0.69         0.26         1.55         0.36         0.30 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
       20.02        54.05         4.01        19.07        21.99        18.94 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 
        1.02        15.02        31.04        55.04         3.58         9.63 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        6.61         4.14         3.65         4.04         2.93         4.27 
TCGA-EQ-8122 TCGA-FP-8631 
        7.79         0.56 

$subtype2
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
        1.35         0.85         0.82         1.71         2.17         0.66 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7957 
        1.12         0.66         1.22         1.05         0.69         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8592 TCGA-CD-5798 
        0.16         1.08         0.49         0.76         0.20         0.82 
TCGA-CD-5803 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 
        0.07        12.00         1.02        65.10         4.54         9.80 
TCGA-EQ-5647 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.62         0.39         3.02         3.58        59.05         5.03 
TCGA-IN-7806 
        6.87 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 
        5.62         0.10         0.95         1.41         1.35         0.62 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 
        0.99         1.22         0.76         0.26         0.46         1.25 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        0.13         0.16         0.99         0.95         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-CD-5799 TCGA-CD-5801 
        0.26         0.43         1.18         1.48         0.69         0.49 
TCGA-CD-5813 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.39         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 
        8.05        14.01        29.98        47.05        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
        4.01        21.07         7.99         8.65        15.65         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-F1-6177 
        6.90         0.69         5.95         1.68         4.70         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-HJ-7597 TCGA-IN-7808 
        2.01        72.23         0.20         1.02        26.43         3.55 
TCGA-IP-7968 
        2.53 

subtype1 subtype2 subtype3 
    0.26     0.07     0.10 
subtype1 subtype2 subtype3 
   55.04    65.10    72.23 
subtype1 subtype2 subtype3 
    3.83     1.05     1.48 
[1] "0.3 - 55.0 (3.8)" "0.1 - 65.1 (1.1)" "0.1 - 72.2 (1.5)"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [55] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[127] "subtype3" "subtype2" "subtype3" "subtype3"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [55] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[127] "subtype3" "subtype2" "subtype3" "subtype3"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [55] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[127] "subtype3" "subtype2" "subtype3" "subtype3"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 14 24
  subtype2 17 25
  subtype3 35 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   24
  subtype2   17   25
  subtype3   35   52
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       17       35
  MALE         24       25       52
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     0
  subtype2                                     5
  subtype3                                     1
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      2
  subtype2                                                      1
  subtype3                                                      4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 5
  subtype2                                                                 0
  subtype3                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        2
  subtype3                                                        0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     2
  subtype2                                     4
  subtype3                                    10
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     13
  subtype2                                                     22
  subtype3                                                     38
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 1
  subtype2                                                 3
  subtype3                                                 4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  2
  subtype2                                                  0
  subtype3                                                  1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                6
  subtype2                                                0
  subtype3                                                4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      7
  subtype2                                                                      3
  subtype3                                                                     18
D6V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0 11 14  4
  subtype2  0  7 16  7
  subtype3  6 34 27  7
D6V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  8  9  7  4
  subtype2 11 12  5  4
  subtype3 26 28 11  7
D6V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 28  2  1
  subtype2 27  4  3
  subtype3 64 10  4
D6V7, multiclass
          vv
clus        I II III IV
  subtype1  3 12   7  6
  subtype2  4  8   9  9
  subtype3 17 18  23 11
D6V8, multiclass
D6V9, binary
          cls
clus        0  1
  subtype1  2 36
  subtype2  2 40
  subtype3  1 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   36
  subtype2    2   40
  subtype3    1   86
     clus
vv    subtype1 subtype2 subtype3
  NO         2        2        1
  YES       36       40       86
          vv
clus       R0 R1 R2 RX
  subtype1 29  1  2  3
  subtype2 27  3  1  7
  subtype3 55  3  9 15
D6V10, multiclass
D6V11, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
                           "PATHOLOGY.T" 
                                      V6 
                           "PATHOLOGY.N" 
                                      V7 
                   "PATHOLOGICSPREAD(M)" 
                                      V8 
                           "TUMOR.STAGE" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V10 
             "COMPLETENESS.OF.RESECTION" 
                                     V11 
                 "NUMBER.OF.LYMPH.NODES" 
> q(save="no")
