
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/2907357/1.GDAC_mergedClustering.Finished/STAD-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/2844303/1.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=178, in cluster file=308, common to both=178
[1]   6 178
[1] "CN_CNMF"
[1] 3
 1  2  3 
88 71 18 
 1  2  3 
88 71 18 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
18 28 38 46 
 1  2  3  4 
18 28 38 46 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
22 21 
 1  2 
22 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
15  7 21 
 1  2  3 
15  7 21 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
84 36 45 
 1  2  3 
84 36 45 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
41 73 51 
 1  2  3 
41 73 51 
[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 178 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-CD-5798 
          13            4            7            3           22           25 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
          21           11           15            9            2           NA 
TCGA-CD-5813 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
          12          609           92          822          485           31 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 
        1611          245         1644          122          426           NA 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
         912         1431          580          366          669           31 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 
         273          576          215          365           31           NA 
TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
          NA           31           31          211           31           31 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
          30          182           29         2131          366          457 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
         881          944         1980          122         1674          641 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
         243          263          109          138          298          476 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
         293          249          210           21          181          201 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
         126           51          111          143          123           89 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
         130           19          237          199           61           NA 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
          12            6           92          109           31           NA 
TCGA-FP-8631 TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 
          17           NA           NA           NA           NA           NA 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
          NA          209          108           77 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=94,	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=7,	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 
26 49 58 29 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 178 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 54 65 43 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 54 65 43 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 54 65 43 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 54 65 43 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
57 61 29 20 
[1] "table(vv)"
vv
N0 N1 N2 N3 
57 61 29 20 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
57 61 29 20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
57 61 29 20 
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 
 26  49  58  29 
[1] "table(vv)"
vv
  I  II III  IV 
 26  49  58  29 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 26  49  58  29 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 26  49  58  29 
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 62  8
  subtype2 49  7
  subtype3 11  3
subtype1 subtype2 subtype3 
      70       56       14 
subtype1 subtype2 subtype3 
       8        7        3 
$subtype1
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.95         1.41         1.35         0.85         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62         1.71         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.16         0.99         0.69         0.16         1.08         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26         0.43         0.26         1.18         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-CD-5798 
        0.79         0.53         0.43         0.13         0.10         0.82 
TCGA-CD-5803 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 
        0.07         1.02        14.01         1.02         8.98         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         1.02         6.94         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-6522 TCGA-D7-6524 TCGA-F1-6177 
       70.06        65.10         7.99         6.90         0.69         6.54 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-HJ-7597 
        3.02         3.58        59.05        26.43 

$subtype2
TCGA-B7-5818 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
        0.10         1.35         0.62         1.48         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5799 
        0.69         4.54         0.95         0.72         0.72         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        0.36         0.30         3.02         8.05        54.05         4.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 
       29.98        47.05        19.07        12.03        21.99        18.94 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       12.00         1.02         1.02        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       55.04         8.65         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        8.19         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7806 
       72.23         0.39         0.20         1.02         0.56         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

$subtype3
TCGA-BR-6801 TCGA-BR-7704 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 
        1.12         1.25         0.23         0.49        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 
       15.95        52.96         7.07        28.96        31.04        21.07 
TCGA-D7-5578 TCGA-F1-6874 
        3.58         2.01 

subtype1 subtype2 subtype3 
    0.07     0.10     0.23 
subtype1 subtype2 subtype3 
   70.06    72.23    52.96 
subtype1 subtype2 subtype3 
   0.950    4.025   11.510 
[1] "0.1 - 70.1 (0.9)"  "0.1 - 72.2 (4.0)"  "0.2 - 53.0 (11.5)"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 44 44
  subtype2 21 50
  subtype3  5 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   44
  subtype2   21   50
  subtype3    5   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       21        5
  MALE         44       50       13
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                    15
  subtype2                                     9
  subtype3                                     1
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     49
  subtype2                                                     30
  subtype3                                                      8
          vv
clus       STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  subtype1                                         1
  subtype2                                         0
  subtype3                                         0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 5
  subtype2                                                 5
  subtype3                                                 0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  2
  subtype3                                                  0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                0
  subtype2                                                9
  subtype3                                                1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                     15
  subtype2                                                                     13
  subtype3                                                                      8
D1V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  3 18 31 31
  subtype2  1 30 26 10
  subtype3  2  6  7  2
D1V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 30 32 14  7
  subtype2 18 27 12 10
  subtype3  8  2  3  3
D1V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 72 10  6
  subtype2 56  8  7
  subtype3 18  0  0
D1V7, multiclass
          vv
clus        I II III IV
  subtype1 11 24  32 13
  subtype2 10 20  20 15
  subtype3  5  4   6  1
D1V8, multiclass
D1V9, binary
          cls
clus        0  1
  subtype1  1 87
  subtype2  4 67
  subtype3  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   87
  subtype2    4   67
  subtype3    0   18
     clus
vv    subtype1 subtype2 subtype3
  NO         1        4        0
  YES       87       67       18
          vv
clus       R0 R1 R2 RX
  subtype1 62  2  6 15
  subtype2 47  4  6  8
  subtype3 14  1  0  2
D1V10, multiclass
D1V11, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 18  0
  subtype2 22  4
  subtype3 32  4
  subtype4 36  5
subtype1 subtype2 subtype3 subtype4 
      18       26       36       41 
subtype1 subtype2 subtype3 subtype4 
       0        4        4        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-CG-4437 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        0.72         8.05         0.99        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 
       21.07         5.95         1.68         4.27         6.54         2.01 
TCGA-FP-7829 TCGA-FP-8099 
        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-HJ-7597 TCGA-IN-7808 
        8.19         6.90         0.69        59.05        26.43         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    0.970    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" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [67] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
 [73] "subtype4" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype4" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype4" "subtype4" "subtype2" "subtype1" "subtype1"
[115] "subtype2" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[121] "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" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [67] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
 [73] "subtype4" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype4" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype4" "subtype4" "subtype2" "subtype1" "subtype1"
[115] "subtype2" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[121] "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" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [67] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
 [73] "subtype4" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype4"
 [85] "subtype4" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype4" "subtype4" "subtype2" "subtype1" "subtype1"
[115] "subtype2" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[121] "subtype4"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  7 11
  subtype2  9 19
  subtype3 15 23
  subtype4 17 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   11
  subtype2    9   19
  subtype3   15   23
  subtype4   17   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7        9       15       17
  MALE         11       19       23       29
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     4
  subtype2                                     3
  subtype3                                    13
  subtype4                                     3
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     11
  subtype2                                                     11
  subtype3                                                     14
  subtype4                                                     22
          vv
clus       STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  subtype1                                         0
  subtype2                                         0
  subtype3                                         1
  subtype4                                         0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 0
  subtype2                                                 3
  subtype3                                                 4
  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                                                                      2
  subtype2                                                                      8
  subtype3                                                                      6
  subtype4                                                                     11
D2V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  2  7  9
  subtype2  4 10  9  5
  subtype3  0 10 16 12
  subtype4  0 17 21  8
D2V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  8  4  3  3
  subtype2 14  7  3  4
  subtype3 12 14  9  3
  subtype4 15 18  8  5
D2V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 13  3  2
  subtype2 25  1  2
  subtype3 33  4  1
  subtype4 38  3  5
D2V7, multiclass
          vv
clus        I II III IV
  subtype1  1  4  10  3
  subtype2 10  9   7  2
  subtype3  4 13  16  5
  subtype4  4 18  16  8
D2V8, multiclass
D2V9, binary
          cls
clus        0  1
  subtype1  0 18
  subtype2  1 27
  subtype3  0 38
  subtype4  4 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   18
  subtype2    1   27
  subtype3    0   38
  subtype4    4   42
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        0        4
  YES       18       27       38       42
          vv
clus       R0 R1 R2
  subtype1 15  0  1
  subtype2 27  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 5 2
  subtype2 8 3
subtype1 subtype2 
       7       11 
subtype1 subtype2 
       2        3 
$subtype1
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        3.02        15.95         1.02        19.07        21.99         1.02 
TCGA-CG-4472 
       12.00 

$subtype2
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
       27.02        52.96        54.05         4.01        29.98        47.05 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07         1.02         1.02 

subtype1 subtype2 
    1.02     1.02 
subtype1 subtype2 
   21.99    54.05 
subtype1 subtype2 
   12.00    18.94 
[1] "1.0 - 22.0 (12.0)" "1.0 - 54.0 (18.9)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[1] "hr=" "1.5"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  9 13
  subtype2 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   13
  subtype2   11   10
        clus
vv       subtype1 subtype2
  FEMALE        9       11
  MALE         13       10
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     1
  subtype2                                     1
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     15
  subtype2                                                     10
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 1
  subtype2                                                 0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                1
  subtype2                                                0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      1
  subtype2                                                                      8
D3V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  6  6  6
  subtype2  2  8  3  3
D3V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  2 10  2  2
  subtype2  6  4  3  3
D3V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 16  4  2
  subtype2 18  3  0
D3V7, multiclass
          vv
clus       I II III IV
  subtype1 1  4   3  6
  subtype2 6  0   3  5
D3V8, multiclass
D3V9, binary
          cls
clus        0
  subtype1 22
  subtype2 21
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  4 13
  subtype2  8  1  3  9
D3V10, multiclass
D3V11, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 6 3
  subtype2 2 0
  subtype3 5 2
subtype1 subtype2 subtype3 
       9        2        7 
subtype1 subtype2 subtype3 
       3        0        2 
$subtype1
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4465 
       27.02        52.96        54.05         4.01        47.05         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 
       18.94         7.07         1.02 

$subtype2
TCGA-CG-4443 TCGA-CG-4477 
       29.98         1.02 

$subtype3
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        3.02        15.95         1.02        19.07        21.99         1.02 
TCGA-CG-4472 
       12.00 

subtype1 subtype2 subtype3 
    1.02     1.02     1.02 
subtype1 subtype2 subtype3 
   54.05    29.98    21.99 
subtype1 subtype2 subtype3 
   18.94    15.50    12.00 
[1] "1.0 - 54.0 (18.9)" "1.0 - 30.0 (15.5)" "1.0 - 22.0 (12.0)"
 [1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       9        2        7 
 [1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype3" "subtype1"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  8  7
  subtype2  3  4
  subtype3  9 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    7
  subtype2    3    4
  subtype3    9   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        3        9
  MALE          7        4       12
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     1
  subtype2                                     0
  subtype3                                     1
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      7
  subtype2                                                      4
  subtype3                                                     14
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 0
  subtype2                                                 0
  subtype3                                                 1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                0
  subtype2                                                0
  subtype3                                                1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                      5
  subtype2                                                                      3
  subtype3                                                                      1
D4V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  6  3  3
  subtype2  1  3  1  0
  subtype3  0  5  5  6
D4V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  3  2  3  3
  subtype2  4  2  0  0
  subtype3  1 10  2  2
D4V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 12  3  0
  subtype2  6  0  1
  subtype3 16  4  1
D4V7, multiclass
          vv
clus       I II III IV
  subtype1 3  0   3  5
  subtype2 4  0   0  0
  subtype3 0  4   3  6
D4V8, multiclass
D4V9, binary
          cls
clus        0
  subtype1 15
  subtype2  7
  subtype3 21
[1] "NOT AVAILABLE: table only has an event [0]"
          vv
clus       R0 R1 R2 RX
  subtype1  5  1  3  6
  subtype2  3  0  0  4
  subtype3  5  0  4 12
D4V10, multiclass
D4V11, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        3        6 
[1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[8] "subtype3" "subtype3"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 50 12
  subtype2 27  2
  subtype3 34  3
subtype1 subtype2 subtype3 
      62       29       37 
subtype1 subtype2 subtype3 
      12        2        3 
$subtype1
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-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7722 
        0.99         1.22         1.12         0.76         0.26         0.16 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        0.26         1.18         1.48         0.69         0.49         0.30 
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-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-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        31.04         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 
        7.99         8.65        15.65         8.19         0.69         5.95 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        1.68         3.65         4.70         0.62         6.54         2.01 
TCGA-HJ-7597 TCGA-IN-7808 
       26.43         3.55 

$subtype2
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
        1.35         0.85         0.82         0.62         1.71         2.17 
TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 
        0.66         0.66         1.22         0.69         1.08         0.82 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8592 TCGA-CD-5798 TCGA-CD-5803 
        0.49         0.72         0.76         0.20         0.82         0.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       12.00         6.94        65.10         4.54         9.80         9.63 
TCGA-D7-6522 TCGA-D7-6818 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        6.90         4.04         3.02         3.58        59.05 

$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-4300 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 
        0.36        20.02        54.05        21.99        18.94        15.02 
TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 
        3.58         6.61         4.14         2.93         4.27         7.79 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7806 
       72.23         0.39         0.20         1.02         0.56         6.87 
TCGA-IP-7968 
        2.53 

subtype1 subtype2 subtype3 
    0.10     0.07     0.13 
subtype1 subtype2 subtype3 
   70.06    65.10    72.23 
subtype1 subtype2 subtype3 
   2.515    1.220    1.250 
[1] "0.1 - 70.1 (2.5)" "0.1 - 65.1 (1.2)" "0.1 - 72.2 (1.2)"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype1" "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" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype1" "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" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype3" "subtype1" "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" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 37 47
  subtype2 14 22
  subtype3 15 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   47
  subtype2   14   22
  subtype3   15   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37       14       15
  MALE         47       22       30
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                    10
  subtype2                                    10
  subtype3                                     1
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     40
  subtype2                                                     16
  subtype3                                                     24
          vv
clus       STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  subtype1                                         1
  subtype2                                         0
  subtype3                                         0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 4
  subtype3                                                 3
          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                                                                     22
  subtype2                                                                      4
  subtype3                                                                     10
D5V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  4 33 29 13
  subtype2  0  9 14 10
  subtype3  2 11 19 11
D5V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 24 29 13 10
  subtype2  9 13  5  8
  subtype3 20 15  7  1
D5V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 65 14  5
  subtype2 32  2  2
  subtype3 37  2  6
D5V7, multiclass
          vv
clus        I II III IV
  subtype1 13 19  24 17
  subtype2  4 10  14  5
  subtype3  9 15  12  7
D5V8, multiclass
D5V9, binary
          cls
clus        0  1
  subtype1  0 84
  subtype2  1 35
  subtype3  4 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   84
  subtype2    1   35
  subtype3    4   41
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        4
  YES       84       35       41
          vv
clus       R0 R1 R2 RX
  subtype1 47  3 11 18
  subtype2 26  2  0  5
  subtype3 37  2  1  2
D5V10, multiclass
D5V11, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 31  3
  subtype2 47  9
  subtype3 33  5
subtype1 subtype2 subtype3 
      34       56       38 
subtype1 subtype2 subtype3 
       3        9        5 
$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-BR-8297 TCGA-CD-5800 
        1.32         0.69         0.26         1.55         0.76         0.36 
TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4460 TCGA-CG-4466 
        0.30        20.02        54.05         4.01        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-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
        6.61         4.14         1.68         3.65         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 
        4.27         7.79         1.02         0.56 

$subtype2
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-7958 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.13         0.16         0.16         0.46         0.26         0.43 
TCGA-BR-8291 TCGA-BR-8296 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 TCGA-CG-4301 
        1.18         1.48         0.69         0.49         0.39         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02        52.96         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        47.05        12.03         1.02         8.98         7.07 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
        1.02         1.02         6.94         5.98         0.95        12.03 
TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
        4.01        21.07         8.65        15.65         8.19         5.95 
TCGA-D7-6817 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-HJ-7597 
        4.70         6.54         2.01        72.23         0.20        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

$subtype3
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-7851 
        1.12         0.66         1.22         1.05         0.69         0.99 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8592 
        0.69         1.08         0.95         0.49         0.72         0.20 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CG-4472 TCGA-CG-5716 TCGA-CG-5719 TCGA-CG-5720 
        0.82         0.07        12.00         1.02         1.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 
       70.06        28.96        65.10         7.99         4.54         9.80 
TCGA-D7-6522 TCGA-D7-6524 TCGA-EQ-5647 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.90         0.69         0.62         0.39         3.02         3.58 
TCGA-FP-8209 TCGA-IN-7806 
       59.05         6.87 

subtype1 subtype2 subtype3 
    0.26     0.10     0.07 
subtype1 subtype2 subtype3 
   55.04    72.23    70.06 
subtype1 subtype2 subtype3 
   3.255    1.745    1.035 
[1] "0.3 - 55.0 (3.3)" "0.1 - 72.2 (1.7)" "0.1 - 70.1 (1.0)"
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [85] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[127] "subtype2" "subtype2"
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [85] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[127] "subtype2" "subtype2"
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [85] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[127] "subtype2" "subtype2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 15 26
  subtype2 32 41
  subtype3 19 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   26
  subtype2   32   41
  subtype3   19   32
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       32       19
  MALE         26       41       32
          vv
clus       STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  subtype1                                     3
  subtype2                                     9
  subtype3                                     9
          vv
clus       STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     16
  subtype2                                                     37
  subtype3                                                     27
          vv
clus       STOMACH ADENOCARCINOMA - SIGNET RING TYPE
  subtype1                                         0
  subtype2                                         1
  subtype3                                         0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  subtype1                                                 0
  subtype2                                                 3
  subtype3                                                 6
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  subtype1                                                  2
  subtype2                                                  1
  subtype3                                                  0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  subtype1                                                8
  subtype2                                                2
  subtype3                                                0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                     12
  subtype2                                                                     17
  subtype3                                                                      7
D6V4, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0 12 17 10
  subtype2  5 28 26 10
  subtype3  1 13 19 14
D6V5, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 11 13  8  5
  subtype2 26 24 11  7
  subtype3 16 20  6  7
D6V6, multiclass
          vv
clus       M0 M1 MX
  subtype1 34  3  4
  subtype2 57 10  6
  subtype3 43  5  3
D6V7, multiclass
          vv
clus        I II III IV
  subtype1  4 14  11  8
  subtype2 15 16  23 11
  subtype3  7 14  16 10
D6V8, multiclass
D6V9, binary
          cls
clus        0  1
  subtype1  2 39
  subtype2  1 72
  subtype3  2 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   39
  subtype2    1   72
  subtype3    2   49
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1        2
  YES       39       72       49
          vv
clus       R0 R1 R2 RX
  subtype1 31  1  2  4
  subtype2 45  2  8 13
  subtype3 34  4  2  8
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")
