
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.75.4002/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.75.4002/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD-TP/2404281/1.GDAC_mergedClustering.Finished/STAD-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/2332215/1.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=162, in cluster file=257, common to both=162
[1]   6 162
[1] "CN_CNMF"
[1] 3
 1  2  3 
21 73 67 
 1  2  3 
21 73 67 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
24 11 29 33 
 1  2  3  4 
24 11 29 33 
[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 
51 34 49 
 1  2  3 
51 34 49 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
43 34 57 
 1  2  3 
43 34 57 
[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] "BATCHNUMBER"                           

Input Data has 15 rows and 162 columns.

[1] "Batch" "15"   
[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-CD-5798 TCGA-CD-5799 
          36           47           45           23           25           21 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
          11           15            9            2           NA           12 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
         609           92          822          485           31         1611 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 
         245         1644          122          426           NA          912 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1431          580          366          669           31          273 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 
         576          215          365           31           NA           NA 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          31           31          211           31           31           30 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
         182           29         2131          366          457          881 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
         944         1980          122         1674          641          243 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
         263          109          138          298          476          293 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
         249          210           21          181          201          126 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
          51          111          143          123           89          130 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
          19          237          199           61           NA           12 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 
           6           92          109           NA           NA           NA 
TCGA-HF-7134 TCGA-HF-7136 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
          NA           NA           NA          209          108           77 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=88,	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:'BATCH.NUMBER':	nDistinctValues=9,	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"
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
25 44 48 29 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 162 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=44, 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 53 60 33 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 53 60 33 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 53 60 33 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 53 60 33 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
51 57 24 19 
[1] "table(vv)"
vv
N0 N1 N2 N3 
51 57 24 19 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
51 57 24 19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
51 57 24 19 
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 
 25  44  48  29 
[1] "table(vv)"
vv
  I  II III  IV 
 25  44  48  29 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 25  44  48  29 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 25  44  48  29 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  7  3
  subtype2 50  7
  subtype3 51  6
subtype1 subtype2 subtype3 
      10       57       57 
subtype1 subtype2 subtype3 
       3        7        6 
$subtype1
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6705 TCGA-BR-6707 TCGA-CG-4305 
        5.62         0.95         1.41         1.71         0.99        15.95 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-5726 TCGA-CG-5733 
       14.01        12.03        28.96        21.07 

$subtype2
TCGA-B7-5818 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         1.35         0.62         1.12         1.48         1.25 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-CD-5799 
        1.05         0.82         0.69         4.54         0.95         0.69 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
        0.36         0.30        20.02         3.02        27.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05         4.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 
       21.99        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 
       12.03        15.02        31.04         4.01        55.04         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
        4.54         9.80        15.65         9.63         8.19         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        6.61         4.14         1.68         3.65         4.70         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        4.27         0.62         7.79        72.23         0.39         0.20 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

$subtype3
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6709 
        1.35         0.85         0.82         0.62         2.17         1.22 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        0.66         0.76         0.66         0.26         1.22         0.46 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.13         0.16         0.99         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4306 
        1.48         0.76         0.82         0.49         0.07         1.02 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        1.02         8.98         1.02         1.02         1.02         6.94 
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-D7-6818 TCGA-F1-6177 TCGA-F1-6874 
        8.65         6.90         0.69         4.04         6.54         2.01 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
        3.02         3.58        26.43 

subtype1 subtype2 subtype3 
    0.95     0.10     0.07 
subtype1 subtype2 subtype3 
   28.96    72.23    70.06 
subtype1 subtype2 subtype3 
   8.825    4.270    0.990 
[1] "0.9 - 29.0 (8.8)" "0.1 - 72.2 (4.3)" "0.1 - 70.1 (1.0)"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 12  9
  subtype2 21 52
  subtype3 32 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    9
  subtype2   21   52
  subtype3   32   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       21       32
  MALE          9       52       35
D1V4, multiclass
D1V5, multiclass
D1V6, multiclass
D1V7, multiclass
D1V8, multiclass
D1V9, binary
          cls
clus        0  1
  subtype1  0 21
  subtype2  3 70
  subtype3  2 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   21
  subtype2    3   70
  subtype3    2   65
     clus
vv    subtype1 subtype2 subtype3
  NO         0        3        2
  YES       21       70       65

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 18  4
  subtype2 11  0
  subtype3 23  3
  subtype4 25  4
subtype1 subtype2 subtype3 subtype4 
      22       11       26       29 
subtype1 subtype2 subtype3 subtype4 
       4        0        3        4 
$subtype1
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7707 
        5.62         0.95         1.35         0.62         0.46         0.13 
TCGA-BR-7717 TCGA-BR-7851 TCGA-CG-4437 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5724 
        0.69         0.99         8.05         0.99         5.98        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       28.96        65.10        21.07         0.69         5.95         1.68 
TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 
        4.27         6.54         2.01         0.20 

$subtype2
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7196 
        0.10         1.41         2.17         0.99         0.26         1.22 
TCGA-CD-5801 TCGA-CG-5722 TCGA-D7-5577 TCGA-FP-7916 TCGA-FP-7998 
        0.49         0.95         8.65         3.02         3.58 

$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-7716 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5802 
        0.76         0.66         0.82         0.69         0.82         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5723 
        0.07         0.39         1.02         6.94         1.02        70.06 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 
        7.99         4.54         9.80         8.19         6.90         4.04 
TCGA-HJ-7597 TCGA-IN-7808 
       26.43         3.55 

$subtype4
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 
        0.62         1.12         1.48         1.25         1.05         0.16 
TCGA-BR-7723 TCGA-BR-7901 TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4441 TCGA-CG-5718 
        4.54         0.95         0.69         0.36        14.01         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 
       15.02        31.04         4.01        55.04         3.58        15.65 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        9.63         6.61         4.14         3.65         4.70         2.93 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-IN-7806 TCGA-IP-7968 
        0.62        72.23         0.39         6.87         2.53 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.10     0.07     0.16 
subtype1 subtype2 subtype3 subtype4 
   65.10     8.65    70.06    72.23 
subtype1 subtype2 subtype3 subtype4 
   1.845    1.220    1.120    3.580 
[1] "0.1 - 65.1 (1.8)" "0.1 - 8.7 (1.2)"  "0.1 - 70.1 (1.1)" "0.2 - 72.2 (3.6)"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype4" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
[25] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
[31] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype1" "subtype2"
[49] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype1"
[55] "subtype4" "subtype4" "subtype1" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
[73] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[79] "subtype1" "subtype4" "subtype4" "subtype1" "subtype2" "subtype2"
[85] "subtype3" "subtype4" "subtype3" "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype4" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
[25] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
[31] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype1" "subtype2"
[49] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype1"
[55] "subtype4" "subtype4" "subtype1" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
[73] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[79] "subtype1" "subtype4" "subtype4" "subtype1" "subtype2" "subtype2"
[85] "subtype3" "subtype4" "subtype3" "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype4" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
[25] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
[31] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype1" "subtype2"
[49] "subtype3" "subtype1" "subtype4" "subtype1" "subtype4" "subtype1"
[55] "subtype4" "subtype4" "subtype1" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
[73] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[79] "subtype1" "subtype4" "subtype4" "subtype1" "subtype2" "subtype2"
[85] "subtype3" "subtype4" "subtype3" "subtype4"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  8 16
  subtype2  3  8
  subtype3 10 19
  subtype4 11 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   16
  subtype2    3    8
  subtype3   10   19
  subtype4   11   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8        3       10       11
  MALE         16        8       19       22
D2V4, multiclass
D2V5, multiclass
D2V6, multiclass
D2V7, multiclass
D2V8, multiclass
D2V9, binary
          cls
clus        0  1
  subtype1  1 23
  subtype2  0 11
  subtype3  1 28
  subtype4  3 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    0   11
  subtype3    1   28
  subtype4    3   30
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        1        3
  YES       23       11       28       30

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
D3V4, multiclass
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass
D3V9, binary
          cls
clus        0
  subtype1 22
  subtype2 21
[1] "NOT AVAILABLE: table only has an event [0]"

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
D4V4, multiclass
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
D4V9, binary
          cls
clus        0
  subtype1 15
  subtype2  7
  subtype3 21
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 34 10
  subtype2 23  1
  subtype3 25  4
subtype1 subtype2 subtype3 
      44       24       29 
subtype1 subtype2 subtype3 
      10        1        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-CD-5799 
        0.62         0.99         1.22         0.76         0.26         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CG-4306 TCGA-CG-4437 
        0.36         0.49         0.30         0.39         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 
       54.05         4.01        14.01        29.98        12.03        21.99 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
       18.94         1.02         5.98        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       31.04         4.01        21.07         7.99         8.65        15.65 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6820 
        9.63         0.69         5.95         6.61         1.68         2.93 
TCGA-D7-6822 TCGA-EQ-5647 
        4.27         0.62 

$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-CD-5798 TCGA-CD-5803 
        1.12         0.66         1.22         1.05         0.82         0.07 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         6.94         1.02         0.95        70.06 
TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 
       65.10         4.54         9.80         8.19         6.90         4.04 

$subtype3
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        0.46         1.25         0.13         0.82         0.69         4.54 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4444 
       20.02         3.02        27.02        15.95        52.96        47.05 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5720 
        1.02         8.98         7.07        12.00         1.02         0.99 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-F1-6177 
       55.04         3.58         4.14         3.65         4.70         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7806 
        2.01        72.23         0.39         0.20         6.87 

subtype1 subtype2 subtype3 
    0.10     0.07     0.13 
subtype1 subtype2 subtype3 
   54.05    70.06    72.23 
subtype1 subtype2 subtype3 
    4.01     1.17     4.14 
[1] "0.1 - 54.0 (4.0)" "0.1 - 70.1 (1.2)" "0.1 - 72.2 (4.1)"
 [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" "subtype2"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[67] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[73] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[79] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[97] "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" "subtype2"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[67] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[73] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[79] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[97] "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" "subtype2"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[67] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[73] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[79] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[97] "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 22 29
  subtype2 13 21
  subtype3 17 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   29
  subtype2   13   21
  subtype3   17   32
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       13       17
  MALE         29       21       32
D5V4, multiclass
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
D5V9, binary
          cls
clus        0  1
  subtype1  0 51
  subtype2  1 33
  subtype3  4 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   51
  subtype2    1   33
  subtype3    4   45
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        4
  YES       51       33       45

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 28  4
  subtype2 22  4
  subtype3 32  7
subtype1 subtype2 subtype3 
      32       26       39 
subtype1 subtype2 subtype3 
       4        4        7 
$subtype1
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-CD-5798 
        1.12         0.66         1.22         1.05         0.69         0.82 
TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        0.07         3.02        12.00         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5734 
        1.02         0.95        70.06        28.96        65.10         7.99 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-EQ-5647 
        4.54         9.80         8.19         6.90         0.69         0.62 
TCGA-FP-7735 TCGA-IN-7806 
        0.39         6.87 

$subtype2
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7723 TCGA-CD-5800 TCGA-CD-5802 
        0.62         1.22         0.82         4.54         0.36         0.30 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4460 
       20.02        15.95         1.02        54.05         4.01        21.99 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-5578 
       18.94         1.02        15.02        31.04        55.04         3.58 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        9.63         6.61         4.14         1.68         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 
        2.93         4.27 

$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-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.99         0.76         0.26         0.46         1.25         0.13 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
        0.69         0.49         0.39        27.02        52.96         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        47.05        12.03         1.02         8.98 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5730 
        7.07         1.02         0.99         5.98        12.03         4.01 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6817 TCGA-F1-6177 
       21.07         8.65        15.65         5.95         4.70         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        2.01        72.23         0.20 

subtype1 subtype2 subtype3 
    0.07     0.30     0.10 
subtype1 subtype2 subtype3 
   70.06    55.04    72.23 
subtype1 subtype2 subtype3 
    1.17     4.09     4.01 
[1] "0.1 - 70.1 (1.2)" "0.3 - 55.0 (4.1)" "0.1 - 72.2 (4.0)"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[73] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[79] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[85] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[97] "subtype1"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[73] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[79] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[85] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[97] "subtype1"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[73] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[79] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[85] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[91] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[97] "subtype1"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 15 28
  subtype2 12 22
  subtype3 25 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   28
  subtype2   12   22
  subtype3   25   32
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       12       25
  MALE         28       22       32
D6V4, multiclass
D6V5, multiclass
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass
D6V9, binary
          cls
clus        0  1
  subtype1  1 42
  subtype2  3 31
  subtype3  1 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   42
  subtype2    3   31
  subtype3    1   56
     clus
vv    subtype1 subtype2 subtype3
  NO         1        3        1
  YES       42       31       56
                                    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" 
> q(save="no")
