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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LIHC-TP/3144268/1.GDAC_mergedClustering.Finished/LIHC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC-TP/3132685/1.GDAC_clinicalDataPicker.Finished/LIHC-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=73, in cluster file=99, common to both=73
[1]  6 73
[1] "CN_CNMF"
[1] 3
 1  2  3 
18 26 28 
 1  2  3 
18 26 28 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
20 21 31 
 1  2  3 
20 21 31 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6  7  8  9 
16  7  6 11 11  3  4  1  1 
 1  2  3  4  5  6  7 
16  7  6 11 11  3  4 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2 
26 34 
 1  2 
26 34 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
28 14 29 
 1  2  3 
28 14 29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2 
 8 63 
 1  2 
 8 63 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "COMPLETENESS.OF.RESECTION"        "BATCHNUMBER"                     

Input Data has 12 rows and 73 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          352           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
          NA         1144          420            8          252            2 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
          NA            2            3            4         1678           NA 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
          NA           NA          693           NA           79           NA 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
         652           NA           NA         2414         2017          601 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
        1628          203         1036          183          887           NA 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
         129          110          111           60           NA           97 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
          13           NA           NA           NA           NA            4 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
          37         1175         1231          434          390         1359 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
          NA          269          253          192          179          136 
TCGA-G3-A3CK 
          27 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "COMPLETENESS.OF.RESECTION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 73 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 10  7
  subtype2 15  8
  subtype3 15 11
subtype1 subtype2 subtype3 
      17       23       26 
subtype1 subtype2 subtype3 
       7        8       11 
$subtype1
TCGA-BC-4072 TCGA-BC-A10U TCGA-CC-5258 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 
       48.99        27.52         0.07         0.13        55.17        22.78 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J 
        7.33        90.67         6.67         6.02        13.64         4.24 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-G3-A3CG TCGA-G3-A3CJ 
        0.62         3.19        14.40         8.32         4.47 

$subtype2
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 
       11.57        37.32        10.13        46.78        25.32        69.57 
TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       37.74         0.46        51.25        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-EP-A26S TCGA-EP-A3RK TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U 
       53.52         3.62         0.43         0.13        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.27        12.82         6.31         5.88         0.89 

$subtype3
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 
       27.52         2.99        23.34         1.12         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
       13.81         0.26         8.28         4.24         0.07         0.10 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ 
       83.57        53.29         2.60        21.44        34.06        29.16 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25X 
        3.65         1.97        22.85        19.07         1.22        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z 
       14.86         8.84 

subtype1 subtype2 subtype3 
    0.07     0.13     0.07 
subtype1 subtype2 subtype3 
   90.67    79.36    83.57 
subtype1 subtype2 subtype3 
   7.330   19.760   11.325 
[1] "0.1 - 90.7 (7.3)"  "0.1 - 79.4 (19.8)" "0.1 - 83.6 (11.3)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[61] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[61] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[61] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  4 14
  subtype2 12 14
  subtype3  9 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   14
  subtype2   12   14
  subtype3    9   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       12        9
  MALE         14       14       19
          vv
clus       R0 R1 R2 RX
  subtype1 12  3  1  1
  subtype2 18  2  0  2
  subtype3 20  3  0  5
D1V4, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  8  8
  subtype2 12  7
  subtype3 20 10
subtype1 subtype2 subtype3 
      16       19       30 
subtype1 subtype2 subtype3 
       8        7       10 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10X TCGA-BC-A110 TCGA-DD-A114 
       48.99        11.57        37.32        25.32        69.57        37.74 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EL TCGA-EP-A3RK TCGA-ES-A2HT 
       90.67        19.76        53.52        13.64         0.43        14.40 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI 
       38.63        14.27        12.82         5.88 

$subtype2
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-A3MA TCGA-CC-A3MC 
       10.13         2.99         5.03         0.07         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EB 
       55.17        53.29        22.78         7.33         0.46        66.31 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-EP-A2KB TCGA-FV-A3R3 TCGA-G3-A25X TCGA-G3-A25Y 
       34.06         6.02         1.97         0.13        44.68        14.86 
TCGA-G3-A3CH 
        6.31 

$subtype3
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       46.78        27.52        27.52        23.34         1.12        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A115 
       13.81         0.26         8.28         4.24         0.10        83.57 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EJ 
        2.60        21.44        51.25        79.36         6.67        29.16 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QR 
        4.24         3.62         3.65         0.62         3.19        19.07 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK 
        1.22        40.47         8.84         8.32         4.47         0.89 

subtype1 subtype2 subtype3 
    0.43     0.07     0.10 
subtype1 subtype2 subtype3 
   90.67    66.31    83.57 
subtype1 subtype2 subtype3 
   22.54     6.31     8.30 
[1] "0.4 - 90.7 (22.5)" "0.1 - 66.3 (6.3)"  "0.1 - 83.6 (8.3)" 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[55] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[55] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[55] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  9 11
  subtype2  8 13
  subtype3  9 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   11
  subtype2    8   13
  subtype3    9   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        8        9
  MALE         11       13       22
          vv
clus       R0 R1 R2 RX
  subtype1 13  3  0  1
  subtype2 15  1  1  4
  subtype3 21  4  0  4
D2V4, multiclass

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 6 7
  subtype2 4 3
  subtype3 3 2
  subtype4 4 7
  subtype5 7 4
  subtype6 3 0
  subtype7 4 0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      13        7        5       11       11        3        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       7        3        2        7        4        0        0 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 
       48.99        11.57        37.32         2.99         5.03        37.61 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A1EC TCGA-EP-A2KA TCGA-G3-A25T TCGA-G3-A25X 
        4.24        37.74        19.76         3.65        38.63        44.68 
TCGA-G3-A25Y 
       14.86 

$subtype2
TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-ES-A2HT TCGA-FV-A3R3 
       10.13        55.17        22.78         7.33        14.40         0.13 
TCGA-G3-A3CH 
        6.31 

$subtype3
TCGA-BC-A10S TCGA-BC-A10X TCGA-DD-A1EI TCGA-G3-A25V TCGA-G3-A25Z 
       46.78        25.32         6.02        14.27         8.84 

$subtype4
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-DD-A115 TCGA-DD-A11B 
       27.52        23.34         1.12         0.26        83.57         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-ES-A2HS TCGA-G3-A25U 
       21.44        51.25        66.31        22.85        40.47 

$subtype5
TCGA-BC-A10U TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       27.52        53.29        79.36        53.52         6.67        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.24         3.62         0.62         4.47         0.89 

$subtype6
TCGA-BC-A217 TCGA-BC-A3KG TCGA-G3-A25S 
       13.81         8.28         1.22 

$subtype7
TCGA-CC-5258 TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-EP-A2KB 
        0.07        34.06        29.16         1.97 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    2.99     0.13     6.02     0.26     0.62     1.22     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   48.99    55.17    46.78    83.57    79.36    13.81    34.06 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  19.760   10.130   14.270   23.340    6.670    8.280   15.565 
[1] "3.0 - 49.0 (19.8)" "0.1 - 55.2 (10.1)" "6.0 - 46.8 (14.3)"
[4] "0.3 - 83.6 (23.3)" "0.6 - 79.4 (6.7)"  "1.2 - 13.8 (8.3)" 
[7] "0.1 - 34.1 (15.6)"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
 [7] "subtype5" "subtype1" "subtype3" "subtype4" "subtype4" "subtype1"
[13] "subtype1" "subtype6" "subtype4" "subtype6" "subtype7" "subtype1"
[19] "subtype2" "subtype1" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype4" "subtype4" "subtype4" "subtype5" "subtype4" "subtype1"
[31] "subtype5" "subtype5" "subtype7" "subtype3" "subtype7" "subtype5"
[37] "subtype5" "subtype5" "subtype1" "subtype7" "subtype5" "subtype4"
[43] "subtype2" "subtype2" "subtype6" "subtype1" "subtype4" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
 [7] "subtype5" "subtype1" "subtype3" "subtype4" "subtype4" "subtype1"
[13] "subtype1" "subtype6" "subtype4" "subtype6" "subtype7" "subtype1"
[19] "subtype2" "subtype1" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype4" "subtype4" "subtype4" "subtype5" "subtype4" "subtype1"
[31] "subtype5" "subtype5" "subtype7" "subtype3" "subtype7" "subtype5"
[37] "subtype5" "subtype5" "subtype1" "subtype7" "subtype5" "subtype4"
[43] "subtype2" "subtype2" "subtype6" "subtype1" "subtype4" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
 [7] "subtype5" "subtype1" "subtype3" "subtype4" "subtype4" "subtype1"
[13] "subtype1" "subtype6" "subtype4" "subtype6" "subtype7" "subtype1"
[19] "subtype2" "subtype1" "subtype4" "subtype5" "subtype2" "subtype2"
[25] "subtype4" "subtype4" "subtype4" "subtype5" "subtype4" "subtype1"
[31] "subtype5" "subtype5" "subtype7" "subtype3" "subtype7" "subtype5"
[37] "subtype5" "subtype5" "subtype1" "subtype7" "subtype5" "subtype4"
[43] "subtype2" "subtype2" "subtype6" "subtype1" "subtype4" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  8  8
  subtype2  4  3
  subtype3  1  5
  subtype4  5  6
  subtype5  0 11
  subtype6  2  1
  subtype7  2  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    8
  subtype2    4    3
  subtype3    1    5
  subtype4    5    6
  subtype5    0   11
  subtype6    2    1
  subtype7    2    2
          vv
clus       R0 R1 R2 RX
  subtype1  8  4  0  3
  subtype2  6  0  1  0
  subtype3  5  0  0  0
  subtype4  8  1  0  2
  subtype5  9  1  0  0
  subtype6  2  1  0  0
  subtype7  3  0  0  1
D3V4, multiclass

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 15  8
  subtype2 17 15
subtype1 subtype2 
      23       32 
subtype1 subtype2 
       8       15 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 
       48.99        11.57        37.32        10.13         2.99         5.03 
TCGA-BC-A216 TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
       37.61         0.07         4.24         0.10        55.17        37.74 
TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A2KA 
       22.78        19.76        34.06         6.02        29.16         3.65 
TCGA-EP-A2KB TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
        1.97         0.13        38.63        44.68        14.86 

$subtype2
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.34         1.12 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
       13.81         0.26         8.28        83.57        53.29         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.44        51.25        79.36        66.31        53.52 
TCGA-DD-A1EE TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-ES-A2HS 
        6.67        13.64         4.24         3.62         0.62        22.85 
TCGA-ES-A2HT TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH 
       14.40         1.22        40.47        14.27         8.84         6.31 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

subtype1 subtype2 
    0.07     0.26 
subtype1 subtype2 
   55.17    83.57 
subtype1 subtype2 
   14.86    14.04 
[1] "0.1 - 55.2 (14.9)" "0.3 - 83.6 (14.0)"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[55] "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[55] "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[55] "subtype2"
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 14 12
  subtype2  9 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   12
  subtype2    9   25
        clus
vv       subtype1 subtype2
  FEMALE       14        9
  MALE         12       25
          vv
clus       R0 R1 R2 RX
  subtype1 17  4  0  4
  subtype2 26  3  1  2
D4V4, multiclass

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 14 11
  subtype2  5  6
  subtype3 20  8
subtype1 subtype2 subtype3 
      25       11       28 
subtype1 subtype2 subtype3 
      11        6        8 
$subtype1
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 
       48.99        37.32        10.13        27.52        25.32        69.57 
TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        5.03         0.07         0.07         0.10         0.13        37.74 
TCGA-DD-A119 TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-EP-A2KA TCGA-ES-A2HT 
        7.33        53.52        34.06         6.02         3.65        14.40 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       38.63        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CH 
        6.31 

$subtype2
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A10Z TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A1EL 
       11.57        23.34         1.12         4.24        83.57        13.64 
TCGA-EP-A3JL TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A3CG TCGA-G3-A3CI 
        3.19        19.07         1.22         8.32         5.88 

$subtype3
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       46.78        27.52         2.99        37.61        13.81         0.26 
TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        8.28        55.17        53.29        22.78         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EE 
       21.44        51.25        79.36        66.31        19.76         6.67 
TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       29.16         4.24         3.62         1.97         0.62         0.43 
TCGA-ES-A2HS TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK 
       22.85        40.47         4.47         0.89 

subtype1 subtype2 subtype3 
    0.07     1.12     0.26 
subtype1 subtype2 subtype3 
   69.57    83.57    79.36 
subtype1 subtype2 subtype3 
  14.270    8.320   16.785 
[1] "0.1 - 69.6 (14.3)" "1.1 - 83.6 (8.3)"  "0.3 - 79.4 (16.8)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[61] "subtype1" "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[61] "subtype1" "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[61] "subtype1" "subtype2" "subtype3" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 11 17
  subtype2  2 12
  subtype3 12 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   17
  subtype2    2   12
  subtype3   12   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11        2       12
  MALE         17       12       17
          vv
clus       R0 R1 R2 RX
  subtype1 20  3  1  4
  subtype2  6  3  0  2
  subtype3 22  2  0  3
D5V4, multiclass

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  3
  subtype2 36 22
subtype1 subtype2 
       6       58 
subtype1 subtype2 
       3       22 
$subtype1
TCGA-BC-4073 TCGA-BC-A10Z TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A3JL TCGA-G3-A25S 
       11.57         1.12        83.57        13.64         3.19         1.22 

$subtype2
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        55.17        37.74        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        7.33         2.60         0.46        21.44        51.25        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       29.16         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U 
        0.43        22.85        14.40        19.07        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

subtype1 subtype2 
    1.12     0.07 
subtype1 subtype2 
   83.57    79.36 
subtype1 subtype2 
    7.38    14.04 
[1] "1.1 - 83.6 (7.4)"  "0.1 - 79.4 (14.0)"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  1  7
  subtype2 24 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2   24   39
        clus
vv       subtype1 subtype2
  FEMALE        1       24
  MALE          7       39
          vv
clus       R0 R1 R2 RX
  subtype1  3  2  0  0
  subtype2 45  6  1  9
D6V4, multiclass
                       V1.D                          V2 
            "Time to Death"                       "AGE" 
                         V3                          V4 
                   "GENDER" "COMPLETENESS.OF.RESECTION" 
> q(save="no")
