
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.59.3844/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.59.3844/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM/1712878/1.GDAC_mergedClustering.Finished/SKCM.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/1669670/1.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=251, common to both=137
[1]   5 137
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
15 37 46 38 
 1  2  3  4 
15 37 46 38 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
43 40 42 
 1  2  3 
43 40 42 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
57 31 37 
 1  2  3 
57 31 37 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
56 46 31 
 1  2  3 
56 46 31 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
16 29 88 
 1  2  3 
16 29 88 
[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] "NEOADJUVANTTHERAPY"                    
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 137 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-DA-A1HV 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
          NA           NA           NA           NA           NA           NA 
TCGA-EB-A24D TCGA-EB-A299 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19O 
          NA           NA           NA           NA         1340           NA 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        2433         2443           NA           NA           NA           NA 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZN 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FW-A3I3 TCGA-GF-A2C7 TCGA-GN-A262 
          NA           NA           NA            6           NA         3664 
TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
          NA           NA         2577           NA           NA           NA 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
          NA           NA           NA         1204           NA 
Variable 1:'AGE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=11,	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=4,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=6,	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 137 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=18, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = METHLYATION_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 1 3
  subtype2 1 2
  subtype3 3 4
  subtype4 1 2
subtype1 subtype2 subtype3 subtype4 
       4        3        7        3 
subtype1 subtype2 subtype3 subtype4 
       3        2        4        2 
$subtype1
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A267 TCGA-GN-A26D 
       12.59       131.08        64.41        39.58 

$subtype2
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A268 
       80.32       117.93        62.76 

$subtype3
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A269 
       44.05        79.99        15.35        84.72        10.09         5.59 
TCGA-GN-A26C 
       26.99 

$subtype4
TCGA-ER-A19F TCGA-GN-A262 TCGA-GN-A26A 
       26.37       120.46        32.48 

subtype1 subtype2 subtype3 subtype4 
   12.59    62.76     5.59    26.37 
subtype1 subtype2 subtype3 subtype4 
  131.08   117.93    84.72   120.46 
subtype1 subtype2 subtype3 subtype4 
  51.995   80.320   26.990   32.480 
[1] "12.6 - 131.1 (52.0)" "62.8 - 117.9 (80.3)" "5.6 - 84.7 (27.0)"  
[4] "26.4 - 120.5 (32.5)"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
 [1] "subtype1" "subtype4" "subtype1" "subtype3" "subtype3" "subtype2"
 [7] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   12
  subtype2   15   22
  subtype3   10   36
  subtype4   17   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3       15       10       17
  MALE         12       22       36       21

Clustering(2) Variable = MRNASEQ_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 0 5
  subtype2 2 4
  subtype3 3 1
subtype1 subtype2 subtype3 
       5        6        4 
subtype1 subtype2 subtype3 
       5        4        1 
$subtype1
TCGA-ER-A19F TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       26.37        15.35       117.93        64.41        62.76 

$subtype2
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       12.59       131.08       120.46        10.09        32.48        39.58 

$subtype3
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A265 TCGA-GN-A26C 
       44.05        79.99        84.72        26.99 

subtype1 subtype2 subtype3 
   15.35    10.09    26.99 
subtype1 subtype2 subtype3 
  117.93   131.08    84.72 
subtype1 subtype2 subtype3 
   62.76    36.03    62.02 
[1] "15.3 - 117.9 (62.8)" "10.1 - 131.1 (36.0)" "27.0 - 84.7 (62.0)" 
 [1] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype2"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   31
  subtype2   17   23
  subtype3   14   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       17       14
  MALE         31       23       28

Clustering(3) Variable = MRNASEQ_CHIERARCHICAL
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 3
  subtype2 1 2
  subtype3 1 5
subtype1 subtype2 subtype3 
       6        3        6 
subtype1 subtype2 subtype3 
       3        2        5 
$subtype1
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A267 
       26.37        44.05        79.99        15.35        84.72        64.41 

$subtype2
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
      117.93        62.76        39.58 

$subtype3
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26C 
       12.59       131.08       120.46        10.09        32.48        26.99 

subtype1 subtype2 subtype3 
   15.35    39.58    10.09 
subtype1 subtype2 subtype3 
   84.72   117.93   131.08 
subtype1 subtype2 subtype3 
  54.230   62.760   29.735 
[1] "15.3 - 84.7 (54.2)"  "39.6 - 117.9 (62.8)" "10.1 - 131.1 (29.7)"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2"
D3V2, continuous
D3V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   36
  subtype2    9   22
  subtype3   13   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21        9       13
  MALE         36       22       24

Clustering(4) Variable = MIRSEQ_CNMF
D4V1, survival
          sevent
clus2      0 1
  subtype1 0 3
  subtype2 2 6
  subtype3 4 1
subtype1 subtype2 subtype3 
       3        8        5 
subtype1 subtype2 subtype3 
       3        6        1 
$subtype1
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
      117.93        64.41        62.76 

$subtype2
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A3ET TCGA-GN-A263 TCGA-GN-A266 
       12.59       131.08        44.05        80.32        15.35        10.09 
TCGA-GN-A26A TCGA-GN-A26C 
       32.48        26.99 

$subtype3
TCGA-ER-A19F TCGA-ER-A1A1 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 
       26.37        79.99         0.20       120.46        84.72 

subtype1 subtype2 subtype3 
   62.76    10.09     0.20 
subtype1 subtype2 subtype3 
  117.93   131.08   120.46 
subtype1 subtype2 subtype3 
  64.410   29.735   79.990 
[1] "62.8 - 117.9 (64.4)" "10.1 - 131.1 (29.7)" "0.2 - 120.5 (80.0)" 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype1" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype1" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[13] "subtype1" "subtype1" "subtype2" "subtype2"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   37
  subtype2   14   32
  subtype3   11   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       19       14       11
  MALE         37       32       20

Clustering(5) Variable = MIRSEQ_CHIERARCHICAL
D5V1, survival
          sevent
clus2      0 1
  subtype1 2 0
  subtype2 2 4
  subtype3 2 6
subtype1 subtype2 subtype3 
       2        6        8 
subtype1 subtype2 subtype3 
       0        4        6 
$subtype1
TCGA-FW-A3I3 TCGA-GN-A265 
        0.20        84.72 

$subtype2
TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26C 
       12.59        44.05        79.99        10.09        32.48        26.99 

$subtype3
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 
       26.37       131.08        80.32       120.46        15.35       117.93 
TCGA-GN-A267 TCGA-GN-A268 
       64.41        62.76 

subtype1 subtype2 subtype3 
    0.20    10.09    15.35 
subtype1 subtype2 subtype3 
   84.72    79.99   131.08 
subtype1 subtype2 subtype3 
  42.460   29.735   72.365 
[1] "0.2 - 84.7 (42.5)"   "10.1 - 80.0 (29.7)"  "15.3 - 131.1 (72.4)"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype2" "subtype2"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        8 
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype2"
[1] "hr=" "2.2"
D5V2, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        8 
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype2"
D5V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   10
  subtype2    9   20
  subtype3   29   59
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6        9       29
  MALE         10       20       59
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
