
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/LIHC-TP/2284041/1.GDAC_mergedClustering.Finished/LIHC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC-TP/2172555/1.GDAC_clinicalDataPicker.Finished/LIHC-TP.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=62, in cluster file=99, common to both=62
[1]  4 62
[1] "CN_CNMF"
[1] 3
 1  2  3 
15 22 24 
 1  2  3 
15 22 24 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
19 15 27 
 1  2  3 
19 15 27 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
22 12 27 
 1  2  3 
22 12 27 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
 8  9 20 24 
 1  2  3  4 
 8  9 20 24 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "BATCHNUMBER"                     

Input Data has 11 rows and 62 columns.

[1] "Batch" "11"   
[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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
          NA          217           NA           NA           NA          693 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          652           NA           NA 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
         601           NA          129          110          111           60 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
          NA           97           13           NA           NA           NA 
TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
          NA           37         1175         1231          434          390 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
        1359           NA          269          253          192          179 
TCGA-G3-A3CJ TCGA-G3-A3CK 
         136           27 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=14,	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:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 62 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=37, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  7  7
  subtype2 11  8
  subtype3 11 11
subtype1 subtype2 subtype3 
      14       19       22 
subtype1 subtype2 subtype3 
       7        8       11 
$subtype1
TCGA-BC-4072 TCGA-BC-A10U TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 
       48.99        27.52         0.07         7.13        22.78         7.33 
TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
       90.67        13.64         4.24         0.62         3.19        14.40 
TCGA-G3-A3CG TCGA-G3-A3CJ 
        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-A1EC TCGA-EP-A26S TCGA-EP-A3RK 
       37.74         0.46        51.25        19.76         3.62         0.43 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CH TCGA-G3-A3CI 
       38.63        40.47        14.27        12.82         6.31         5.88 
TCGA-G3-A3CK 
        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-DD-A115 TCGA-DD-A116 
       13.81         0.26         8.28         4.24        83.57        53.29 
TCGA-DD-A11A TCGA-DD-A11C TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A2QR 
        2.60        21.44         3.65         1.97        22.85        19.07 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        44.68        14.86         8.84 

subtype1 subtype2 subtype3 
    0.07     0.43     0.26 
subtype1 subtype2 subtype3 
   90.67    69.57    83.57 
subtype1 subtype2 subtype3 
   7.825   14.270   11.325 
[1] "0.1 - 90.7 (7.8)"  "0.4 - 69.6 (14.3)" "0.3 - 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" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  4 11
  subtype2 10 12
  subtype3  8 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   11
  subtype2   10   12
  subtype3    8   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       10        8
  MALE         11       12       16

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  7  8
  subtype2  6  7
  subtype3 16 10
subtype1 subtype2 subtype3 
      15       13       26 
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-A1EL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-G3-A25T 
       90.67        19.76        13.64         0.43        14.40        38.63 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI 
       14.27        12.82         5.88 

$subtype2
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A116 
       10.13         2.99         5.03         0.07         7.13        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-EP-A2KB TCGA-G3-A25X TCGA-G3-A25Y 
       22.78         7.33         0.46         1.97        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-DD-A115 TCGA-DD-A11A 
       13.81         0.26         8.28         4.24        83.57         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       21.44        51.25         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG 
        3.19        19.07         1.22        40.47         8.84         8.32 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

subtype1 subtype2 subtype3 
    0.43     0.07     0.26 
subtype1 subtype2 subtype3 
   90.67    53.29    83.57 
subtype1 subtype2 subtype3 
   19.76     7.13     8.30 
[1] "0.4 - 90.7 (19.8)" "0.1 - 53.3 (7.1)"  "0.3 - 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" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[49] "subtype3" "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" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[49] "subtype3" "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" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[49] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  9 10
  subtype2  6  9
  subtype3  8 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   10
  subtype2    6    9
  subtype3    8   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        6        8
  MALE         10        9       19

Clustering(3) Variable = MIRSEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  8 11
  subtype2  5  4
  subtype3 16 10
subtype1 subtype2 subtype3 
      19        9       26 
subtype1 subtype2 subtype3 
      11        4       10 
$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-DD-A114 TCGA-DD-A119 TCGA-EP-A2KA TCGA-ES-A2HT 
        5.03         0.07        37.74         7.33         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-A10Z TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A3JL 
       11.57         1.12         4.24        83.57        13.64         3.19 
TCGA-G3-A25S TCGA-G3-A3CG TCGA-G3-A3CI 
        1.22         8.32         5.88 

$subtype3
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 
       46.78        27.52         2.99        23.34        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.26         8.28         7.13        53.29        22.78         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S 
        0.46        21.44        51.25        19.76         4.24         3.62 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QR TCGA-G3-A25U 
        1.97         0.62         0.43        22.85        19.07        40.47 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

subtype1 subtype2 subtype3 
    0.07     1.12     0.26 
subtype1 subtype2 subtype3 
   69.57    83.57    53.29 
subtype1 subtype2 subtype3 
  14.400    5.880   11.045 
[1] "0.1 - 69.6 (14.4)" "1.1 - 83.6 (5.9)"  "0.3 - 53.3 (11.0)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 11 11
  subtype2  2 10
  subtype3 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   11
  subtype2    2   10
  subtype3   10   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11        2       10
  MALE         11       10       17

Clustering(4) Variable = MIRSEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  6  2
  subtype2  3  4
  subtype3  6 11
  subtype4 14  8
subtype1 subtype2 subtype3 subtype4 
       8        7       17       22 
subtype1 subtype2 subtype3 subtype4 
       2        4       11        8 
$subtype1
TCGA-BC-A3KF TCGA-DD-A116 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK 
        0.26        53.29         4.24         3.62         0.62         0.43 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

$subtype2
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A3JL 
       48.99        11.57         1.12        83.57        13.64         3.19 
TCGA-G3-A25S 
        1.22 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5258 
       37.32         2.99        25.32        69.57         5.03         0.07 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       37.74         7.33         0.46        19.76         1.97        22.85 
TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       14.40        38.63        44.68        14.86         6.31 

$subtype4
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A216 
       10.13        46.78        27.52        27.52        23.34        37.61 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A 
       13.81         8.28         4.24         7.13        22.78         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-EP-A2KA TCGA-FV-A2QR TCGA-G3-A25U TCGA-G3-A25V 
       21.44        51.25         3.65        19.07        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82         8.84         8.32         5.88 

subtype1 subtype2 subtype3 subtype4 
    0.26     1.12     0.07     2.60 
subtype1 subtype2 subtype3 subtype4 
   53.29    83.57    69.57    51.25 
subtype1 subtype2 subtype3 subtype4 
   2.255   11.570   14.860   14.040 
[1] "0.3 - 53.3 (2.3)"  "1.1 - 83.6 (11.6)" "0.1 - 69.6 (14.9)"
[4] "2.6 - 51.2 (14.0)"
 [1] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
[13] "subtype3" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype4"
[25] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
[37] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[49] "subtype4" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
 [1] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
[13] "subtype3" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype4"
[25] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
[37] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[49] "subtype4" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
 [1] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
[13] "subtype3" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype4"
[25] "subtype3" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
[37] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype2"
[43] "subtype3" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[49] "subtype4" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  1  7
  subtype2  2  7
  subtype3  9 11
  subtype4 11 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2    2    7
  subtype3    9   11
  subtype4   11   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        9       11
  MALE          7        7       11       13
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
