
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.73.3976/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.73.3976/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD/2025410/1.GDAC_mergedClustering.Finished/STAD.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD/1972820/1.GDAC_clinicalDataPicker.Finished/STAD.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-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=159, in cluster file=162, common to both=159
[1]   6 159
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
68 16 12 26 36 
 1  2  3  4  5 
68 16 12 26 36 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
26 21 20 28 
 1  2  3  4 
26 21 20 28 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
11  6  7 11 12 10 
 1  2  3  4  5  6 
11  6  7 11 12 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
11 18 17 11 
 1  2  3  4 
11 18 17 11 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
29 43 24 24 30 
 1  2  3  4  5 
29 43 24 24 30 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
52 55 43 
 1  2  3 
52 55 43 
[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] "NEOADJUVANTTHERAPY"                    
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 159 columns.

[1] "Batch" "16"   
[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-4190 TCGA-BR-4191 TCGA-BR-4194 TCGA-BR-4195 TCGA-BR-4199 TCGA-BR-4200 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4259 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4261 TCGA-BR-4265 TCGA-BR-4267 TCGA-BR-4277 TCGA-BR-4278 TCGA-BR-4279 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4280 TCGA-BR-4281 TCGA-BR-4284 TCGA-BR-4291 TCGA-BR-4292 TCGA-BR-4294 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4298 TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4367 TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-4375 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4376 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 
          NA           29           NA           NA           43           NA 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
          41           41           26           25           19           19 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
          52           66           30           37           20           34 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
          23           20            8           37           45           14 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
          38            4           32           25           21            5 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5799 
         138           30           29           21           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-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
          19          199           61           NA           12            6 
TCGA-FP-7998 TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 
         109           NA           NA           NA           NA           NA 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
         209          108           77 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	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:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=7,	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] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
24 38 43 26 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 159 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 52 62 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 52 62 18 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 52 62 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 52 62 18 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
45 57 24 15 
[1] "table(vv)"
vv
N0 N1 N2 N3 
45 57 24 15 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
45 57 24 15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
45 57 24 15 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE',vnm)"
vv
  I  II III  IV 
 24  38  43  26 
[1] "table(vv)"
vv
  I  II III  IV 
 24  38  43  26 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 24  38  43  26 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 24  38  43  26 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 39  7
  subtype2 12  2
  subtype3  2  2
  subtype4 17  0
  subtype5 20  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      46       14        4       17       24 
subtype1 subtype2 subtype3 subtype4 subtype5 
       7        2        2        0        4 
$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-7851 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4305 
        0.99         0.69         0.82         0.49         0.07        15.95 
TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         1.02         8.98         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        6.94         0.99         5.98         0.95        70.06        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 
       65.10        21.07         7.99         8.65         9.80         6.90 
TCGA-D7-6524 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7998 
        0.69         6.54         2.01         3.58 

$subtype2
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-CG-4300 
        0.10         0.62         1.12         1.48         1.25        20.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 
       27.02        52.96         4.01        18.94         7.07         1.02 
TCGA-CG-5727 TCGA-D7-5578 
       31.04         3.58 

$subtype3
TCGA-BR-6458 TCGA-CG-4441 TCGA-CG-4460 TCGA-FP-7829 
        1.35        14.01        21.99         0.20 

$subtype4
TCGA-BR-7722 TCGA-BR-7723 TCGA-CD-5799 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 
        0.16         4.54         0.69         3.02         8.05        29.98 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 
       12.03        12.00         1.02        55.04        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-IN-7806 
        8.19         5.95         3.65         4.70         6.87 

$subtype5
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-CD-5800 TCGA-CD-5802 
        1.05         0.82         0.69         0.95         0.36         0.30 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       54.05        47.05        19.07        12.03        15.02         4.01 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
        4.54         6.61         4.14         1.68         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-IN-7808 TCGA-IP-7968 
        4.27         0.62        72.23         0.39         3.55         2.53 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.10     0.20     0.16     0.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
   70.06    52.96    21.99    55.04    72.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
   1.020    3.795    7.680    6.870    3.780 
[1] "0.1 - 70.1 (1.0)" "0.1 - 53.0 (3.8)" "0.2 - 22.0 (7.7)" "0.2 - 55.0 (6.9)"
[5] "0.3 - 72.2 (3.8)"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [25] "subtype5" "subtype5" "subtype5" "subtype4" "subtype4" "subtype1"
 [31] "subtype5" "subtype1" "subtype1" "subtype4" "subtype5" "subtype1"
 [37] "subtype5" "subtype1" "subtype2" "subtype4" "subtype2" "subtype1"
 [43] "subtype1" "subtype2" "subtype4" "subtype5" "subtype2" "subtype3"
 [49] "subtype4" "subtype5" "subtype5" "subtype4" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
 [73] "subtype1" "subtype5" "subtype4" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype5" "subtype1" "subtype4" "subtype4" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype5" "subtype5" "subtype5"
 [91] "subtype4" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype1"
[103] "subtype4" "subtype5" "subtype5"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [25] "subtype5" "subtype5" "subtype5" "subtype4" "subtype4" "subtype1"
 [31] "subtype5" "subtype1" "subtype1" "subtype4" "subtype5" "subtype1"
 [37] "subtype5" "subtype1" "subtype2" "subtype4" "subtype2" "subtype1"
 [43] "subtype1" "subtype2" "subtype4" "subtype5" "subtype2" "subtype3"
 [49] "subtype4" "subtype5" "subtype5" "subtype4" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
 [73] "subtype1" "subtype5" "subtype4" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype5" "subtype1" "subtype4" "subtype4" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype5" "subtype5" "subtype5"
 [91] "subtype4" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype1"
[103] "subtype4" "subtype5" "subtype5"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [25] "subtype5" "subtype5" "subtype5" "subtype4" "subtype4" "subtype1"
 [31] "subtype5" "subtype1" "subtype1" "subtype4" "subtype5" "subtype1"
 [37] "subtype5" "subtype1" "subtype2" "subtype4" "subtype2" "subtype1"
 [43] "subtype1" "subtype2" "subtype4" "subtype5" "subtype2" "subtype3"
 [49] "subtype4" "subtype5" "subtype5" "subtype4" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype1"
 [61] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
 [73] "subtype1" "subtype5" "subtype4" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype5" "subtype1" "subtype4" "subtype4" "subtype4"
 [85] "subtype1" "subtype1" "subtype4" "subtype5" "subtype5" "subtype5"
 [91] "subtype4" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype1"
[103] "subtype4" "subtype5" "subtype5"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 31 37
  subtype2  5 11
  subtype3  8  4
  subtype4  7 19
  subtype5  9 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   37
  subtype2    5   11
  subtype3    8    4
  subtype4    7   19
  subtype5    9   27
D1V4, multiclass
D1V5, multiclass
D1V6, multiclass
D1V7, multiclass
D1V8, multiclass
D1V9, binary
          cls
clus        0  1
  subtype1  1 67
  subtype2  0 16
  subtype3  0 12
  subtype4  1 25
  subtype5  3 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   67
  subtype2    0   16
  subtype3    0   12
  subtype4    1   25
  subtype5    3   33
D1V10, binary
          cls
clus        0  1
  subtype1  2 66
  subtype2  0 16
  subtype3  0 12
  subtype4  4 22
  subtype5  5 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   66
  subtype2    0   16
  subtype3    0   12
  subtype4    4   22
  subtype5    5   31

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 20  4
  subtype2 20  0
  subtype3 13  4
  subtype4 23  2
subtype1 subtype2 subtype3 subtype4 
      24       20       17       25 
subtype1 subtype2 subtype3 subtype4 
       4        0        4        2 
$subtype1
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7703 
        5.62         0.95         1.35         0.62         0.76         0.46 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 TCGA-CG-4437 TCGA-CG-5720 TCGA-CG-5721 
        0.13         0.69         0.99         8.05         0.99         5.98 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-6524 
       12.03        28.96        65.10        21.07         3.58         0.69 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 
        5.95         1.68         4.27         6.54         2.01         0.20 

$subtype2
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6852 
        0.10         1.41         0.62         2.17         0.99         0.26 
TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7901 TCGA-CD-5801 TCGA-CG-5718 
        1.22         1.25         0.82         0.95         0.49         1.02 
TCGA-CG-5722 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
        0.95        55.04         8.65         9.63         6.61         4.14 
TCGA-D7-6817 TCGA-FP-7998 
        4.70         3.58 

$subtype3
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7723 TCGA-CD-5799 TCGA-CD-5800 
        1.12         1.48         1.05         4.54         0.69         0.36 
TCGA-CG-4441 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-6815 
       14.01        15.02        31.04         4.01        15.65         3.65 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6875 TCGA-IN-7806 TCGA-IP-7968 
        2.93         0.62        72.23         6.87         2.53 

$subtype4
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-6803 TCGA-BR-7722 TCGA-BR-7957 TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 
        0.66         0.16         0.69         0.82         0.30         0.07 
TCGA-CD-5813 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5734 
        0.39         1.02         6.94         1.02        70.06         7.99 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-FP-7735 
        4.54         9.80         8.19         6.90         4.04         0.39 
TCGA-IN-7808 
        3.55 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.10     0.36     0.07 
subtype1 subtype2 subtype3 subtype4 
   65.10    55.04    72.23    70.06 
subtype1 subtype2 subtype3 subtype4 
   1.845    1.235    3.650    1.020 
[1] "0.1 - 65.1 (1.8)" "0.1 - 55.0 (1.2)" "0.4 - 72.2 (3.6)" "0.1 - 70.1 (1.0)"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [7] "subtype4" "subtype4" "subtype2" "subtype1" "subtype4" "subtype2"
[13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype1" "subtype4"
[19] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype4" "subtype3" "subtype1"
[31] "subtype2" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
[37] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
[43] "subtype4" "subtype2" "subtype4" "subtype1" "subtype1" "subtype2"
[49] "subtype4" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[61] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype4"
[67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[73] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype3" "subtype4" "subtype1" "subtype2" "subtype3"
[85] "subtype4" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [7] "subtype4" "subtype4" "subtype2" "subtype1" "subtype4" "subtype2"
[13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype1" "subtype4"
[19] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype4" "subtype3" "subtype1"
[31] "subtype2" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
[37] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
[43] "subtype4" "subtype2" "subtype4" "subtype1" "subtype1" "subtype2"
[49] "subtype4" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[61] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype4"
[67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[73] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype3" "subtype4" "subtype1" "subtype2" "subtype3"
[85] "subtype4" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [7] "subtype4" "subtype4" "subtype2" "subtype1" "subtype4" "subtype2"
[13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype1" "subtype4"
[19] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype4" "subtype3" "subtype1"
[31] "subtype2" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
[37] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
[43] "subtype4" "subtype2" "subtype4" "subtype1" "subtype1" "subtype2"
[49] "subtype4" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[61] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype4"
[67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[73] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype3" "subtype4" "subtype1" "subtype2" "subtype3"
[85] "subtype4" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  8 18
  subtype2  8 13
  subtype3  7 13
  subtype4  8 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   18
  subtype2    8   13
  subtype3    7   13
  subtype4    8   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8        8        7        8
  MALE         18       13       13       20
D2V4, multiclass
D2V5, multiclass
D2V6, multiclass
D2V7, multiclass
D2V8, multiclass
D2V9, binary
          cls
clus        0  1
  subtype1  1 25
  subtype2  1 20
  subtype3  2 18
  subtype4  1 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   25
  subtype2    1   20
  subtype3    2   18
  subtype4    1   27
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        2        1
  YES       25       20       18       27
D2V10, binary
          cls
clus        0  1
  subtype1  2 24
  subtype2  3 18
  subtype3  3 17
  subtype4  3 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   24
  subtype2    3   18
  subtype3    3   17
  subtype4    3   25
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        3        3        3
  YES       24       18       17       25

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 2 0
  subtype2 2 0
  subtype3 1 0
  subtype4 1 1
  subtype5 2 2
  subtype6 5 2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        1        2        4        7 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       0        0        0        1        2        2 
$subtype1
TCGA-CG-4462 TCGA-CG-4472 
        1.02        12.00 

$subtype2
TCGA-CG-4466 TCGA-CG-4477 
       18.94         1.02 

$subtype3
TCGA-CG-4301 
        3.02 

$subtype4
TCGA-CG-4305 TCGA-CG-4306 
       15.95         1.02 

$subtype5
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        4.01        29.98        19.07        21.99 

$subtype6
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4469 
       27.02        52.96        54.05        47.05         8.98         7.07 
TCGA-CG-4474 
        1.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.02     1.02     3.02     1.02     4.01     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   12.00    18.94     3.02    15.95    29.98    54.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   6.510    9.980    3.020    8.485   20.530   27.020 
[1] "1.0 - 12.0 (6.5)"  "1.0 - 18.9 (10.0)" "3.0 - 3.0 (3.0)"  
[4] "1.0 - 15.9 (8.5)"  "4.0 - 30.0 (20.5)" "1.0 - 54.0 (27.0)"
 [1] "subtype3" "subtype6" "subtype4" "subtype4" "subtype6" "subtype6"
 [7] "subtype5" "subtype5" "subtype6" "subtype5" "subtype5" "subtype1"
[13] "subtype6" "subtype2" "subtype6" "subtype1" "subtype6" "subtype2"
 [1] "subtype3" "subtype6" "subtype4" "subtype4" "subtype6" "subtype6"
 [7] "subtype5" "subtype5" "subtype6" "subtype5" "subtype5" "subtype1"
[13] "subtype6" "subtype2" "subtype6" "subtype1" "subtype6" "subtype2"
 [1] "subtype3" "subtype6" "subtype4" "subtype4" "subtype6" "subtype6"
 [7] "subtype5" "subtype5" "subtype6" "subtype5" "subtype5" "subtype1"
[13] "subtype6" "subtype2" "subtype6" "subtype1" "subtype6" "subtype2"
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        1        2        4        7 
 [1] "subtype6" "subtype6" "subtype6" "subtype5" "subtype5" "subtype6"
 [7] "subtype5" "subtype5" "subtype6" "subtype6" "subtype6"
[1] "hr=" "1.8"
D3V2, continuous
D3V3, binary
          cls
clus       0 1
  subtype1 5 6
  subtype2 4 2
  subtype3 5 2
  subtype4 5 6
  subtype5 4 8
  subtype6 4 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    6
  subtype2    4    2
  subtype3    5    2
  subtype4    5    6
  subtype5    4    8
  subtype6    4    6
D3V4, multiclass
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass
D3V9, binary
          cls
clus        0
  subtype1 11
  subtype2  6
  subtype3  7
  subtype4 11
  subtype5 12
  subtype6 10
[1] "NOT AVAILABLE: table only has an event [0]"
D3V10, binary
          cls
clus        0
  subtype1 11
  subtype2  6
  subtype3  7
  subtype4 11
  subtype5 12
  subtype6 10
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 2 0
  subtype2 4 1
  subtype3 5 3
  subtype4 2 1
subtype1 subtype2 subtype3 subtype4 
       2        5        8        3 
subtype1 subtype2 subtype3 subtype4 
       0        1        3        1 
$subtype1
TCGA-CG-4304 TCGA-CG-4477 
       27.02         1.02 

$subtype2
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-4472 
        3.02        15.95         1.02         1.02        12.00 

$subtype3
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4466 
       52.96        54.05         4.01        47.05         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 
        7.07         1.02 

$subtype4
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
       29.98        19.07        21.99 

subtype1 subtype2 subtype3 subtype4 
    1.02     1.02     1.02    19.07 
subtype1 subtype2 subtype3 subtype4 
   27.02    15.95    54.05    29.98 
subtype1 subtype2 subtype3 subtype4 
   14.02     3.02    13.96    21.99 
[1] "1.0 - 27.0 (14.0)"  "1.0 - 15.9 (3.0)"   "1.0 - 54.0 (14.0)" 
[4] "19.1 - 30.0 (22.0)"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        5        8        3 
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype4" "subtype4" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype3"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  7  4
  subtype2  8 10
  subtype3  9  8
  subtype4  3  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    4
  subtype2    8   10
  subtype3    9    8
  subtype4    3    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7        8        9        3
  MALE          4       10        8        8
D4V4, multiclass
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
D4V9, binary
          cls
clus        0
  subtype1 11
  subtype2 18
  subtype3 17
  subtype4 11
[1] "NOT AVAILABLE: table only has an event [0]"
D4V10, binary
          cls
clus        0
  subtype1 11
  subtype2 18
  subtype3 17
  subtype4 11
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 22  5
  subtype2 11  4
  subtype3 16  2
  subtype4 14  2
  subtype5 19  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      27       15       18       16       21 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        4        2        2        2 
$subtype1
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 
        5.62         0.95         1.41         1.35         0.62         0.99 
TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 
        1.22         0.76         0.26         0.69         0.49         0.39 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5716 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
        8.05        14.01         1.02         1.02         1.02         5.98 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       70.06        12.03        28.96        21.07         7.99         8.65 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
        0.69         5.95         1.68 

$subtype2
TCGA-B7-5818 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 
        4.01        29.98        47.05        12.03         8.98         7.07 
TCGA-CG-4474 TCGA-CG-4477 TCGA-D7-6815 
        1.02         1.02         3.65 

$subtype3
TCGA-BR-6565 TCGA-BR-7715 TCGA-BR-7723 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4438 
        0.62         1.05         4.54         0.36         0.30        54.05 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-6519 
       21.99        18.94        15.02        31.04         4.01        15.65 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6820 TCGA-D7-6822 TCGA-F1-6874 
        9.63         6.61         4.14         2.93         4.27         2.01 

$subtype4
TCGA-BR-6563 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        0.85         0.46         1.25         0.13         0.82         0.69 
TCGA-CG-4436 TCGA-CG-4462 TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6817 TCGA-F1-6177 
       52.96         1.02         0.99         3.58         4.70         6.54 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7806 
       72.23         0.39         0.20         6.87 

$subtype5
TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 
        1.35         0.82         1.71         2.17         0.66         1.12 
TCGA-BR-6803 TCGA-BR-7196 TCGA-CD-5798 TCGA-CD-5803 TCGA-CG-4472 TCGA-CG-5717 
        0.66         1.22         0.82         0.07        12.00         6.94 
TCGA-CG-5722 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        0.95        65.10        55.04         4.54         9.80         8.19 
TCGA-D7-6522 TCGA-D7-6818 TCGA-EQ-5647 
        6.90         4.04         0.62 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.26     0.10     0.30     0.13     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
   70.06    47.05    54.05    72.23    65.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
   1.350    7.070    4.405    1.005    1.710 
[1] "0.3 - 70.1 (1.4)" "0.1 - 47.0 (7.1)" "0.3 - 54.0 (4.4)" "0.1 - 72.2 (1.0)"
[5] "0.1 - 65.1 (1.7)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype5" "subtype1"
 [7] "subtype4" "subtype5" "subtype3" "subtype1" "subtype5" "subtype5"
[13] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype5"
[19] "subtype1" "subtype5" "subtype4" "subtype4" "subtype4" "subtype3"
[25] "subtype4" "subtype4" "subtype3" "subtype5" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype5" "subtype1" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype4" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[55] "subtype2" "subtype1" "subtype5" "subtype1" "subtype1" "subtype4"
[61] "subtype1" "subtype5" "subtype1" "subtype1" "subtype3" "subtype1"
[67] "subtype3" "subtype5" "subtype3" "subtype5" "subtype1" "subtype1"
[73] "subtype1" "subtype4" "subtype5" "subtype5" "subtype3" "subtype3"
[79] "subtype5" "subtype5" "subtype1" "subtype1" "subtype3" "subtype3"
[85] "subtype1" "subtype2" "subtype4" "subtype5" "subtype3" "subtype3"
[91] "subtype5" "subtype4" "subtype3" "subtype4" "subtype4" "subtype4"
[97] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype5" "subtype1"
 [7] "subtype4" "subtype5" "subtype3" "subtype1" "subtype5" "subtype5"
[13] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype5"
[19] "subtype1" "subtype5" "subtype4" "subtype4" "subtype4" "subtype3"
[25] "subtype4" "subtype4" "subtype3" "subtype5" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype5" "subtype1" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype4" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[55] "subtype2" "subtype1" "subtype5" "subtype1" "subtype1" "subtype4"
[61] "subtype1" "subtype5" "subtype1" "subtype1" "subtype3" "subtype1"
[67] "subtype3" "subtype5" "subtype3" "subtype5" "subtype1" "subtype1"
[73] "subtype1" "subtype4" "subtype5" "subtype5" "subtype3" "subtype3"
[79] "subtype5" "subtype5" "subtype1" "subtype1" "subtype3" "subtype3"
[85] "subtype1" "subtype2" "subtype4" "subtype5" "subtype3" "subtype3"
[91] "subtype5" "subtype4" "subtype3" "subtype4" "subtype4" "subtype4"
[97] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype5" "subtype1"
 [7] "subtype4" "subtype5" "subtype3" "subtype1" "subtype5" "subtype5"
[13] "subtype1" "subtype1" "subtype5" "subtype5" "subtype1" "subtype5"
[19] "subtype1" "subtype5" "subtype4" "subtype4" "subtype4" "subtype3"
[25] "subtype4" "subtype4" "subtype3" "subtype5" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype5" "subtype1" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype4" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[55] "subtype2" "subtype1" "subtype5" "subtype1" "subtype1" "subtype4"
[61] "subtype1" "subtype5" "subtype1" "subtype1" "subtype3" "subtype1"
[67] "subtype3" "subtype5" "subtype3" "subtype5" "subtype1" "subtype1"
[73] "subtype1" "subtype4" "subtype5" "subtype5" "subtype3" "subtype3"
[79] "subtype5" "subtype5" "subtype1" "subtype1" "subtype3" "subtype3"
[85] "subtype1" "subtype2" "subtype4" "subtype5" "subtype3" "subtype3"
[91] "subtype5" "subtype4" "subtype3" "subtype4" "subtype4" "subtype4"
[97] "subtype4"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 12 17
  subtype2 22 21
  subtype3  6 18
  subtype4  9 15
  subtype5 10 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   17
  subtype2   22   21
  subtype3    6   18
  subtype4    9   15
  subtype5   10   20
D5V4, multiclass
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
D5V9, binary
          cls
clus        0  1
  subtype1  0 29
  subtype2  0 43
  subtype3  1 23
  subtype4  3 21
  subtype5  1 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   29
  subtype2    0   43
  subtype3    1   23
  subtype4    3   21
  subtype5    1   29
D5V10, binary
          cls
clus        0  1
  subtype1  2 27
  subtype2  0 43
  subtype3  3 21
  subtype4  3 21
  subtype5  3 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   27
  subtype2    0   43
  subtype3    3   21
  subtype4    3   21
  subtype5    3   27

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 30  5
  subtype2 28  6
  subtype3 24  4
subtype1 subtype2 subtype3 
      35       34       28 
subtype1 subtype2 subtype3 
       5        6        4 
$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-7703 TCGA-BR-7715 TCGA-BR-7717 
        1.12         0.66         1.22         0.46         1.05         0.69 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 
        0.82         0.07         3.02        12.00         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        6.94         1.02         0.95        70.06        28.96        65.10 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        7.99         4.54         9.80         8.19         6.90         0.69 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7806 
        0.62        72.23         0.39         0.20         6.87 

$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-7707 TCGA-CD-5799 
        0.99         1.22         0.76         0.26         0.13         0.69 
TCGA-CD-5801 TCGA-CD-5813 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
        0.49         0.39        27.02        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-5720 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5733 TCGA-D7-5577 
        1.02         0.99         5.98        12.03        21.07         8.65 
TCGA-D7-6519 TCGA-D7-6525 TCGA-F1-6177 TCGA-F1-6874 
       15.65         5.95         6.54         2.01 

$subtype3
TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 TCGA-CD-5800 TCGA-CD-5802 
        0.62         1.25         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-5730 TCGA-CG-5732 
       18.94         1.02        15.02        31.04         4.01        55.04 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        3.58         9.63         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.70         4.04         2.93         4.27 

subtype1 subtype2 subtype3 
    0.07     0.10     0.30 
subtype1 subtype2 subtype3 
   72.23    52.96    55.04 
subtype1 subtype2 subtype3 
   1.120    3.815    4.090 
[1] "0.1 - 72.2 (1.1)" "0.1 - 53.0 (3.8)" "0.3 - 55.0 (4.1)"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[97] "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[97] "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[91] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[97] "subtype1"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 18 34
  subtype2 25 30
  subtype3 16 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   34
  subtype2   25   30
  subtype3   16   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       25       16
  MALE         34       30       27
D6V4, multiclass
D6V5, multiclass
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass
D6V9, binary
          cls
clus        0  1
  subtype1  2 50
  subtype2  0 55
  subtype3  3 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   50
  subtype2    0   55
  subtype3    3   40
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        3
  YES       50       55       40
D6V10, binary
          cls
clus        0  1
  subtype1  4 48
  subtype2  3 52
  subtype3  4 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   48
  subtype2    3   52
  subtype3    4   39
     clus
vv    subtype1 subtype2 subtype3
  NO         4        3        4
  YES       48       52       39
                                    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 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
