
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/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/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/6159514/DLBC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/6154398/DLBC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=DLBC-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=DLBC-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/Append_Data/DLBC-TP/6154398/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/6159514/DLBC-TP.mergedcluster.txt"

nPatients in clinical file=21, in cluster file=28, common to both=21
[1]  3 21
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
 3  8 10 
 1  2  3 
 3  8 10 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
12  9 
 1  2 
12  9 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2 
 6 15 
 1  2 
 6 15 
[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] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[12] "RADIATIONTHERAPY"                      
[13] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "GLEASON_SCORE"                         
[16] "PSA_VALUE"                             
[17] "DAYS_TO_PSA"                           
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 21 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
          62         1081          946          965          126          832 
TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
         679          139           NA         1581         1441           NA 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
          NA         3226         5980         3872         2254          812 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
         751          911         1408 
Variable 1:'AGE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=18,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=2,	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 21 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=17, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = METHLYATION_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype2 7 1
  subtype3 7 3
subtype1 subtype2 subtype3 
       3        8       10 
subtype1 subtype2 subtype3 
       0        1        3 
$subtype1
TCGA-FF-8061 TCGA-FF-8062 TCGA-GR-7351 
       27.35        22.32       127.30 

$subtype2
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 
       41.13        51.98        47.38       196.60        74.10        26.70 
TCGA-GR-A4D5 TCGA-GR-A4D6 
       24.69        29.95 

$subtype3
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FM-8000 
        2.04        35.54        31.10        31.73         4.14         4.57 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-A4D9 
      211.23        19.56       106.06        46.29 

subtype1 subtype2 subtype3 
   22.32    24.69     2.04 
subtype1 subtype2 subtype3 
  127.30   196.60   211.23 
subtype1 subtype2 subtype3 
  27.350   44.255   31.415 
[1] "22.3 - 127.3 (27.4)" "24.7 - 196.6 (44.3)" "2.0 - 211.2 (31.4)" 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 4 4
  subtype3 7 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    4    4
  subtype3    7    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        4        7
  MALE          1        4        3

Clustering(2) Variable = MRNASEQ_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 10  2
  subtype2  7  2
subtype1 subtype2 
      12        9 
subtype1 subtype2 
       2        2 
$subtype1
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-G8-6325 TCGA-G8-6326 
        2.04        31.10        31.73        27.35        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D9 
      211.23       106.06       196.60       127.30        26.70        46.29 

$subtype2
TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6907 
       35.54         4.14        22.32         4.57        41.13        19.56 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
       74.10        24.69        29.95 

subtype1 subtype2 
    2.04     4.14 
subtype1 subtype2 
  211.23    74.10 
subtype1 subtype2 
  46.835   24.690 
[1] "2.0 - 211.2 (46.8)" "4.1 - 74.1 (24.7)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1"
[1] "hr="     "2.2e+09"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 5 7
  subtype2 8 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    7
  subtype2    8    1
        clus
vv       subtype1 subtype2
  FEMALE        5        8
  MALE          7        1

Clustering(3) Variable = MRNASEQ_CHIERARCHICAL
D3V1, survival
          sevent
clus2       0  1
  subtype1  4  2
  subtype2 13  2
subtype1 subtype2 
       6       15 
subtype1 subtype2 
       2        2 
$subtype1
TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D6 
        4.14         4.57        41.13        19.56        74.10        29.95 

$subtype2
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 
        2.04        35.54        31.10        31.73        27.35        22.32 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       106.06       196.60       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       26.70        24.69        46.29 

subtype1 subtype2 
    4.14     2.04 
subtype1 subtype2 
   74.10   211.23 
subtype1 subtype2 
  24.755   35.540 
[1] "4.1 - 74.1 (24.8)"  "2.0 - 211.2 (35.5)"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype2"
[1] "hr="     "6.3e+09"
D3V2, continuous
D3V3, binary
          cls
clus       0 1
  subtype1 5 1
  subtype2 8 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2    8    7
        clus
vv       subtype1 subtype2
  FEMALE        5        8
  MALE          1        7
> q(save="no")
