
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/SKCM-TM/2289292/1.GDAC_mergedClustering.Finished/SKCM-TM.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/2173730/1.GDAC_clinicalDataPicker.Finished/SKCM.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=138, in cluster file=237, common to both=126
[1]   8 126
[1] "CN_CNMF"
[1] 3
 1  2  3 
46 43 37 
 1  2  3 
46 43 37 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
32 47 47 
 1  2  3 
32 47 47 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
15 17 17 21 19 
 1  2  3  4  5 
15 17 17 21 19 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
23 15 34 17 
 1  2  3  4 
23 15 34 17 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
43 37 44 
 1  2  3 
43 37 44 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
31 25 68 
 1  2  3 
31 25 68 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
27 43 29 22  2 
 1  2  3  4 
27 43 29 22 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
16 79 28 
 1  2  3 
16 79 28 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [8] "RADIATIONTHERAPY"                      
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "BATCHNUMBER"                           

Input Data has 10 rows and 126 columns.

[1] "Batch" "10"   
[1] "Last Follow UP"
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N 
          NA           NA           NA           NA           NA         1340 
TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
          NA         2433         2443           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
          NA           NA           NA            6         3664           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'BATCH.NUMBER':	nDistinctValues=5,	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 126 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=15, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 5
  subtype2 4 1
  subtype3 0 2
subtype1 subtype2 subtype3 
       8        5        2 
subtype1 subtype2 subtype3 
       5        1        2 
$subtype1
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-FW-A3I3 TCGA-GN-A267 
       12.59        26.37       131.08        44.05         0.20        64.41 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

$subtype2
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       79.99        80.32       120.46        84.72        10.09 

$subtype3
TCGA-GN-A264 TCGA-GN-A26A 
      117.93        32.48 

subtype1 subtype2 subtype3 
    0.20    10.09    32.48 
subtype1 subtype2 subtype3 
  131.08   120.46   117.93 
subtype1 subtype2 subtype3 
  41.815   80.320   75.205 
[1] "0.2 - 131.1 (41.8)"  "10.1 - 120.5 (80.3)" "32.5 - 117.9 (75.2)"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1"
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       8        5        2 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1"
[1] "hr=" "4"  
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 17 29
  subtype2 15 28
  subtype3 14 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   29
  subtype2   15   28
  subtype3   14   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       15       14
  MALE         29       28       23

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 3
  subtype2 1 3
  subtype3 3 2
subtype1 subtype2 subtype3 
       6        4        5 
subtype1 subtype2 subtype3 
       3        3        2 
$subtype1
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3ET TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26D 
       12.59       131.08        80.32         0.20        64.41        39.58 

$subtype2
TCGA-ER-A19F TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       26.37       120.46       117.93        62.76 

$subtype3
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       44.05        79.99        84.72        10.09        32.48 

subtype1 subtype2 subtype3 
    0.20    26.37    10.09 
subtype1 subtype2 subtype3 
  131.08   120.46    84.72 
subtype1 subtype2 subtype3 
  51.995   90.345   44.050 
[1] "0.2 - 131.1 (52.0)"  "26.4 - 120.5 (90.3)" "10.1 - 84.7 (44.0)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype1"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 12 20
  subtype2 21 26
  subtype3 13 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   20
  subtype2   21   26
  subtype3   13   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       21       13
  MALE         20       26       34

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 1 3
  subtype2 0 2
  subtype3 1 0
  subtype4 3 3
subtype1 subtype2 subtype3 subtype4 
       4        2        1        6 
subtype1 subtype2 subtype3 subtype4 
       3        2        0        3 
$subtype1
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A265 TCGA-GN-A266 
       12.59       131.08        84.72        10.09 

$subtype2
TCGA-GN-A267 TCGA-GN-A26A 
       64.41        32.48 

$subtype3
TCGA-ER-A19N 
       44.05 

$subtype4
TCGA-ER-A19F TCGA-ER-A1A1 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       26.37        79.99       120.46       117.93        62.76        39.58 

subtype1 subtype2 subtype3 subtype4 
   10.09    32.48    44.05    26.37 
subtype1 subtype2 subtype3 subtype4 
  131.08    64.41    44.05   120.46 
subtype1 subtype2 subtype3 subtype4 
  48.655   48.445   44.050   71.375 
[1] "10.1 - 131.1 (48.7)" "32.5 - 64.4 (48.4)"  "44.0 - 44.0 (44.0)" 
[4] "26.4 - 120.5 (71.4)"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype4"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype4"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype4"
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       4        2        1        6 
 [1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
 [7] "subtype1" "subtype1" "subtype4" "subtype4"
[1] "hr=" "1.4"
D3V2, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       4        3        1        6 
 [1] "subtype1" "subtype4" "subtype1" "subtype2" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype4"
D3V3, binary
          cls
clus        0  1
  subtype1  5 10
  subtype2  5 12
  subtype3  9  8
  subtype4  8 13
  subtype5  8 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   10
  subtype2    5   12
  subtype3    9    8
  subtype4    8   13
  subtype5    8   11

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 1 0
  subtype2 1 3
  subtype3 2 3
  subtype4 1 2
subtype1 subtype2 subtype3 subtype4 
       1        4        5        3 
subtype1 subtype2 subtype3 subtype4 
       0        3        3        2 
$subtype1
TCGA-ER-A19N 
       44.05 

$subtype2
TCGA-ER-A19D TCGA-ER-A19F TCGA-GN-A266 TCGA-GN-A26D 
       12.59        26.37        10.09        39.58 

$subtype3
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
      131.08        79.99       120.46       117.93        62.76 

$subtype4
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       84.72        64.41        32.48 

subtype1 subtype2 subtype3 subtype4 
   44.05    10.09    62.76    32.48 
subtype1 subtype2 subtype3 subtype4 
   44.05    39.58   131.08    84.72 
subtype1 subtype2 subtype3 subtype4 
   44.05    19.48   117.93    64.41 
[1] "44.0 - 44.0 (44.0)"   "10.1 - 39.6 (19.5)"   "62.8 - 131.1 (117.9)"
[4] "32.5 - 84.7 (64.4)"  
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype4"
[13] "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype4"
[13] "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype4"
[13] "subtype2"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        4        5        3 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype3" "subtype4" "subtype2"
D4V2, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       1        4        5        4 
 [1] "subtype2" "subtype2" "subtype3" "subtype4" "subtype3" "subtype3"
 [7] "subtype3" "subtype4" "subtype2" "subtype4" "subtype3" "subtype4"
[13] "subtype2"
D4V3, binary
          cls
clus        0  1
  subtype1 12 11
  subtype2  4 11
  subtype3 14 20
  subtype4  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   11
  subtype2    4   11
  subtype3   14   20
  subtype4    5   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       12        4       14        5
  MALE         11       11       20       12

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 1 4
  subtype2 3 0
  subtype3 2 4
subtype1 subtype2 subtype3 
       5        3        6 
subtype1 subtype2 subtype3 
       4        0        4 
$subtype1
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A 
       12.59       131.08       120.46        10.09        32.48 

$subtype2
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A265 
       44.05        79.99        84.72 

$subtype3
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       26.37         0.20       117.93        64.41        62.76        39.58 

subtype1 subtype2 subtype3 
   10.09    44.05     0.20 
subtype1 subtype2 subtype3 
  131.08    84.72   117.93 
subtype1 subtype2 subtype3 
   32.48    79.99    51.17 
[1] "10.1 - 131.1 (32.5)" "44.0 - 84.7 (80.0)"  "0.2 - 117.9 (51.2)" 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[13] "subtype1" "subtype3"
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[13] "subtype1" "subtype3"
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[13] "subtype1" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 18 25
  subtype2 11 26
  subtype3 16 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   25
  subtype2   11   26
  subtype3   16   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       11       16
  MALE         25       26       28

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 1 4
  subtype2 2 2
  subtype3 3 2
subtype1 subtype2 subtype3 
       5        4        5 
subtype1 subtype2 subtype3 
       4        2        2 
$subtype1
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A 
       12.59       131.08       120.46        10.09        32.48 

$subtype2
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        0.20       117.93        62.76        39.58 

$subtype3
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A265 TCGA-GN-A267 
       26.37        44.05        79.99        84.72        64.41 

subtype1 subtype2 subtype3 
   10.09     0.20    26.37 
subtype1 subtype2 subtype3 
  131.08   117.93    84.72 
subtype1 subtype2 subtype3 
   32.48    51.17    64.41 
[1] "10.1 - 131.1 (32.5)" "0.2 - 117.9 (51.2)"  "26.4 - 84.7 (64.4)" 
 [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype2"
 [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype2"
 [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 12 19
  subtype2 10 15
  subtype3 23 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   19
  subtype2   10   15
  subtype3   23   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       10       23
  MALE         19       15       45

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 2 1
  subtype2 0 3
  subtype3 1 3
  subtype4 2 1
subtype1 subtype2 subtype3 subtype4 
       3        3        4        3 
subtype1 subtype2 subtype3 subtype4 
       1        3        3        1 
$subtype1
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
      131.08        44.05        79.99 

$subtype2
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
      117.93        64.41        62.76 

$subtype3
TCGA-ER-A19D TCGA-ER-A3ET TCGA-GN-A266 TCGA-GN-A26A 
       12.59        80.32        10.09        32.48 

$subtype4
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A265 
       26.37         0.20        84.72 

subtype1 subtype2 subtype3 subtype4 
   44.05    62.76    10.09     0.20 
subtype1 subtype2 subtype3 subtype4 
  131.08   117.93    80.32    84.72 
subtype1 subtype2 subtype3 subtype4 
  79.990   64.410   22.535   26.370 
[1] "44.0 - 131.1 (80.0)" "62.8 - 117.9 (64.4)" "10.1 - 80.3 (22.5)" 
[4] "0.2 - 84.7 (26.4)"  
 [1] "subtype3" "subtype4" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
[13] "subtype3"
 [1] "subtype3" "subtype4" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
[13] "subtype3"
 [1] "subtype3" "subtype4" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
[13] "subtype3"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 10 17
  subtype2 16 27
  subtype3  8 21
  subtype4  8 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   17
  subtype2   16   27
  subtype3    8   21
  subtype4    8   14
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       16        8        8
  MALE         17       27       21       14

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 2 0
  subtype2 2 5
  subtype3 2 3
subtype1 subtype2 subtype3 
       2        7        5 
subtype1 subtype2 subtype3 
       0        5        3 
$subtype1
TCGA-FW-A3I3 TCGA-GN-A265 
        0.20        84.72 

$subtype2
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       26.37       131.08        80.32       120.46       117.93        64.41 
TCGA-GN-A268 
       62.76 

$subtype3
TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A266 TCGA-GN-A26A 
       12.59        44.05        79.99        10.09        32.48 

subtype1 subtype2 subtype3 
    0.20    26.37    10.09 
subtype1 subtype2 subtype3 
   84.72   131.08    79.99 
subtype1 subtype2 subtype3 
   42.46    80.32    32.48 
[1] "0.2 - 84.7 (42.5)"   "26.4 - 131.1 (80.3)" "10.1 - 80.0 (32.5)" 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype2" "subtype3"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        7        5 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[1] "hr=" "2.6"
D8V2, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        7        5 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
D8V3, binary
          cls
clus        0  1
  subtype1  6 10
  subtype2 29 50
  subtype3  9 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   10
  subtype2   29   50
  subtype3    9   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       29        9
  MALE         10       50       19
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
