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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/UCS-TP/4470420/UCS-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/UCS-TP/4402167/UCS-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=UCS-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oT=UCS-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/UCS-TP/4402167/UCS-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/UCS-TP/4470420/UCS-TP.mergedcluster.txt"

nPatients in clinical file=15, in cluster file=57, common to both=15
[1]  8 15
[1] "CN_CNMF"
[1] 3
1 2 3 4 
4 5 1 4 
1 2 4 
4 5 4 
[1] "METHLYATION_CNMF"
[1] 3
1 2 3 4 5 
3 3 3 1 5 
1 2 3 5 
3 3 3 5 
[1] "MRNASEQ_CNMF"
[1] 3
1 2 3 
6 4 5 
1 2 3 
6 4 5 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 
1 1 5 3 5 
3 4 5 
5 3 5 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 4 
4 6 1 4 
1 2 4 
4 6 4 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
2 3 
8 7 
2 3 
8 7 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 3 4 
4 6 1 4 
1 2 4 
4 6 4 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
2 3 
6 9 
2 3 
6 9 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 15 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-N5-A4R8 TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
          NA         2118         1816           NA           NA          497 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-ND-A4W6 
         424          438          219          145          295           NA 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF 
          NA          461           NA 
Variable 1:'AGE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 15 columns, 1 survival variables, and 1 non-survival variables.
AGE, nv=15, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 1
  subtype2 2 3
  subtype4 3 1
subtype1 subtype2 subtype4 
       4        5        4 
subtype1 subtype2 subtype4 
       1        3        1 
$subtype1
TCGA-N5-A4RT TCGA-N8-A4PN TCGA-N8-A56S TCGA-ND-A4WA 
       69.63        13.94         9.70        23.47 

$subtype2
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PP TCGA-ND-A4W6 TCGA-ND-A4WC 
       14.63        13.71         7.20        10.42        15.16 

$subtype4
TCGA-N5-A4RV TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-ND-A4WF 
       59.70        14.40         4.77         5.49 

subtype1 subtype2 subtype4 
    9.70     7.20     4.77 
subtype1 subtype2 subtype4 
   69.63    15.16    59.70 
subtype1 subtype2 subtype4 
  18.705   13.710    9.945 
[1] "9.7 - 69.6 (18.7)" "7.2 - 15.2 (13.7)" "4.8 - 59.7 (9.9)" 
 [1] "subtype1" "subtype4" "subtype2" "subtype2" "subtype1" "subtype4"
 [7] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype4"
 [1] "subtype1" "subtype4" "subtype2" "subtype2" "subtype1" "subtype4"
 [7] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype4"
 [1] "subtype1" "subtype4" "subtype2" "subtype2" "subtype1" "subtype4"
 [7] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype4"
D1V2, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 2 1
  subtype2 2 1
  subtype3 2 1
  subtype5 2 3
subtype1 subtype2 subtype3 subtype5 
       3        3        3        5 
subtype1 subtype2 subtype3 subtype5 
       1        1        1        3 
$subtype1
TCGA-N5-A4R8 TCGA-N8-A4PN TCGA-N8-A4PQ 
      102.41        13.94         4.77 

$subtype2
TCGA-N5-A4RT TCGA-N5-A4RV TCGA-ND-A4WF 
       69.63        59.70         5.49 

$subtype3
TCGA-N8-A4PI TCGA-N8-A4PP TCGA-ND-A4WC 
       14.63         7.20        15.16 

$subtype5
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A56S TCGA-ND-A4W6 TCGA-ND-A4WA 
       13.71        16.34         9.70        10.42        23.47 

subtype1 subtype2 subtype3 subtype5 
    4.77     5.49     7.20     9.70 
subtype1 subtype2 subtype3 subtype5 
  102.41    69.63    15.16    23.47 
subtype1 subtype2 subtype3 subtype5 
   13.94    59.70    14.63    13.71 
[1] "4.8 - 102.4 (13.9)" "5.5 - 69.6 (59.7)"  "7.2 - 15.2 (14.6)" 
[4] "9.7 - 23.5 (13.7)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype5" "subtype5"
 [7] "subtype1" "subtype3" "subtype1" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype5" "subtype5"
 [7] "subtype1" "subtype3" "subtype1" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype5" "subtype5"
 [7] "subtype1" "subtype3" "subtype1" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype2"
D2V2, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 3
  subtype2 3 1
  subtype3 3 2
subtype1 subtype2 subtype3 
       6        4        5 
subtype1 subtype2 subtype3 
       3        1        2 
$subtype1
TCGA-N5-A4R8 TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-ND-A4W6 TCGA-ND-A4WF 
      102.41        13.94         7.20         4.77        10.42         5.49 

$subtype2
TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-ND-A4WC 
       14.63        16.34        14.40        15.16 

$subtype3
TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N8-A4PL TCGA-N8-A56S TCGA-ND-A4WA 
       69.63        59.70        13.71         9.70        23.47 

subtype1 subtype2 subtype3 
    4.77    14.40     9.70 
subtype1 subtype2 subtype3 
  102.41    16.34    69.63 
subtype1 subtype2 subtype3 
   8.810   14.895   23.470 
[1] "4.8 - 102.4 (8.8)"  "14.4 - 16.3 (14.9)" "9.7 - 69.6 (23.5)" 
 [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype1"
D3V2, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype3 2 3
  subtype4 1 2
  subtype5 4 1
subtype3 subtype4 subtype5 
       5        3        5 
subtype3 subtype4 subtype5 
       3        2        1 
$subtype3
TCGA-N5-A4R8 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-ND-A4W6 TCGA-ND-A4WF 
      102.41        13.94         4.77        10.42         5.49 

$subtype4
TCGA-N8-A4PL TCGA-N8-A56S TCGA-ND-A4WA 
       13.71         9.70        23.47 

$subtype5
TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-ND-A4WC 
       14.63        16.34        14.40         7.20        15.16 

subtype3 subtype4 subtype5 
    4.77     9.70     7.20 
subtype3 subtype4 subtype5 
  102.41    23.47    16.34 
subtype3 subtype4 subtype5 
   10.42    13.71    14.63 
[1] "4.8 - 102.4 (10.4)" "9.7 - 23.5 (13.7)"  "7.2 - 16.3 (14.6)" 
 [1] "subtype3" "subtype5" "subtype4" "subtype5" "subtype3" "subtype5"
 [7] "subtype5" "subtype3" "subtype4" "subtype3" "subtype4" "subtype5"
[13] "subtype3"
 [1] "subtype3" "subtype5" "subtype4" "subtype5" "subtype3" "subtype5"
 [7] "subtype5" "subtype3" "subtype4" "subtype3" "subtype4" "subtype5"
[13] "subtype3"
 [1] "subtype3" "subtype5" "subtype4" "subtype5" "subtype3" "subtype5"
 [7] "subtype5" "subtype3" "subtype4" "subtype3" "subtype4" "subtype5"
[13] "subtype3"
D4V2, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 2 2
  subtype2 2 4
  subtype4 4 0
subtype1 subtype2 subtype4 
       4        6        4 
subtype1 subtype2 subtype4 
       2        4        0 
$subtype1
TCGA-N5-A4R8 TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-ND-A4WF 
      102.41         7.20         4.77         5.49 

$subtype2
TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-ND-A4W6 TCGA-ND-A4WA 
       59.70        14.63        13.71        13.94        10.42        23.47 

$subtype4
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S TCGA-ND-A4WC 
       16.34        14.40         9.70        15.16 

subtype1 subtype2 subtype4 
    4.77    10.42     9.70 
subtype1 subtype2 subtype4 
  102.41    59.70    16.34 
subtype1 subtype2 subtype4 
   6.345   14.285   14.780 
[1] "4.8 - 102.4 (6.3)"  "10.4 - 59.7 (14.3)" "9.7 - 16.3 (14.8)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
D5V2, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype2 6 2
  subtype3 3 4
subtype2 subtype3 
       8        7 
subtype2 subtype3 
       2        4 
$subtype2
TCGA-N5-A4R8 TCGA-N5-A4RT TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
      102.41        69.63        16.34         7.20         4.77         9.70 
TCGA-ND-A4WC TCGA-ND-A4WF 
       15.16         5.49 

$subtype3
TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-ND-A4W6 
       59.70        14.63        13.71        13.94        14.40        10.42 
TCGA-ND-A4WA 
       23.47 

subtype2 subtype3 
    4.77    10.42 
subtype2 subtype3 
  102.41    59.70 
subtype2 subtype3 
   12.43    14.40 
[1] "4.8 - 102.4 (12.4)" "10.4 - 59.7 (14.4)"
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype2" "subtype2"
[1] "hr=" "3.6"
D6V2, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 2 2
  subtype2 2 4
  subtype4 4 0
subtype1 subtype2 subtype4 
       4        6        4 
subtype1 subtype2 subtype4 
       2        4        0 
$subtype1
TCGA-N5-A4R8 TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-ND-A4WF 
      102.41         7.20         4.77         5.49 

$subtype2
TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-ND-A4W6 TCGA-ND-A4WA 
       59.70        14.63        13.71        13.94        10.42        23.47 

$subtype4
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S TCGA-ND-A4WC 
       16.34        14.40         9.70        15.16 

subtype1 subtype2 subtype4 
    4.77    10.42     9.70 
subtype1 subtype2 subtype4 
  102.41    59.70    16.34 
subtype1 subtype2 subtype4 
   6.345   14.285   14.780 
[1] "4.8 - 102.4 (6.3)"  "10.4 - 59.7 (14.3)" "9.7 - 16.3 (14.8)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
[13] "subtype4" "subtype1"
D7V2, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype2 2 4
  subtype3 7 2
subtype2 subtype3 
       6        9 
subtype2 subtype3 
       4        2 
$subtype2
TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-ND-A4W6 TCGA-ND-A4WA 
       59.70        14.63        13.71        13.94        10.42        23.47 

$subtype3
TCGA-N5-A4R8 TCGA-N5-A4RT TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ 
      102.41        69.63        16.34        14.40         7.20         4.77 
TCGA-N8-A56S TCGA-ND-A4WC TCGA-ND-A4WF 
        9.70        15.16         5.49 

subtype2 subtype3 
   10.42     4.77 
subtype2 subtype3 
   59.70   102.41 
subtype2 subtype3 
  14.285   14.400 
[1] "10.4 - 59.7 (14.3)" "4.8 - 102.4 (14.4)"
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3"
[1] "hr=" "4.4"
D8V2, continuous
> q(save="no")
