
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/ACC-TP/6159636/ACC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/6154371/ACC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=ACC-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=ACC-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/ACC-TP/6154371/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/6159636/ACC-TP.mergedcluster.txt"

nPatients in clinical file=10, in cluster file=92, common to both=10
[1] "Reduce the number of clustering variables from 8 to 7."
[1]  7 10
[1] "METHLYATION_CNMF"
[1] 3
1 2 3 4 
2 1 4 3 
3 4 
4 3 
[1] "MRNASEQ_CNMF"
[1] 3
1 2 3 4 
4 2 1 3 
1 4 
4 3 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 
3 4 3 
1 2 3 
3 4 3 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 
4 2 4 
1 3 
4 4 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 
3 3 4 
1 2 3 
3 3 4 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 3 
4 2 4 
1 3 
4 4 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 
4 3 3 
1 2 3 
4 3 3 
[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] "GLEASON_SCORE"                         
[14] "PSA_VALUE"                             
[15] "DAYS_TO_PSA"                           
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 10 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO 
          NA           NA         1423          309           NA          889 
TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
        3688         1130           NA          709 
Variable 1:'AGE':	nDistinctValues=10,	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=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	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:'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:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N"
Output Data has 10 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=10, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=3, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T4 
 3  3  3 
[1] "table(vv)"
vv
T1+T2+T4 
       9 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T4 
 3  3  3 

$nClasses
[1] 1

$ClinVariableType
[1] "multiclass(1)"


T1+T2+T4 
       9 
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = METHLYATION_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype3 3 1
  subtype4 2 1
subtype3 subtype4 
       4        3 
subtype3 subtype4 
       1        1 
$subtype3
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OU-A5PI 
       57.53        46.78        10.16        23.31 

$subtype4
TCGA-OR-A5JB TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        29.23       121.25 

subtype3 subtype4 
   10.16    18.08 
subtype3 subtype4 
   57.53   121.25 
subtype3 subtype4 
  35.045   29.230 
[1] "10.2 - 57.5 (35.0)"  "18.1 - 121.2 (29.2)"
[1] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[1] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[1] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[1] "hr=" "1"  
D1V2, continuous
          vv
clus       STAGE I STAGE IV
  subtype3       1        2
  subtype4       2        1
D1V3, multiclass
          clus
vv         subtype3 subtype4
  STAGE I         1        2
  STAGE IV        2        1
          vv
clus       T1+T2+T4
  subtype3        3
  subtype4        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D1V5, binary
          cls
clus       0 1
  subtype3 1 3
  subtype4 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype3    1    3
  subtype4    1    2
        clus
vv       subtype3 subtype4
  FEMALE        1        1
  MALE          3        2

Clustering(2) Variable = MRNASEQ_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 1 3
  subtype4 3 0
subtype1 subtype4 
       4        3 
subtype1 subtype4 
       3        0 
$subtype1
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.08        18.05        37.15        11.31 

$subtype4
TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR 
       46.78        29.23       121.25 

subtype1 subtype4 
   11.31    29.23 
subtype1 subtype4 
   37.15   121.25 
subtype1 subtype4 
  18.065   46.780 
[1] "11.3 - 37.1 (18.1)"  "29.2 - 121.2 (46.8)"
[1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
[1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
[1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
[1] "hr="     "1.8e+09"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       0        2        2
  subtype4       3        0        0
D2V3, multiclass
          vv
clus       T1+T2+T4
  subtype1        4
  subtype4        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D2V5, binary
          cls
clus       0 1
  subtype1 3 1
  subtype4 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype4    1    2
        clus
vv       subtype1 subtype4
  FEMALE        3        1
  MALE          1        2

Clustering(3) Variable = MRNASEQ_CHIERARCHICAL
D3V1, survival
          sevent
clus2      0 1
  subtype1 1 2
  subtype2 3 1
  subtype3 2 1
subtype1 subtype2 subtype3 
       3        4        3 
subtype1 subtype2 subtype3 
       2        1        1 
$subtype1
TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.05        37.15        11.31 

$subtype2
TCGA-OR-A5JB TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR 
       18.08        46.78        29.23       121.25 

$subtype3
TCGA-OR-A5JC TCGA-OR-A5JJ TCGA-OU-A5PI 
       57.53        10.16        23.31 

subtype1 subtype2 subtype3 
   11.31    18.08    10.16 
subtype1 subtype2 subtype3 
   37.15   121.25    57.53 
subtype1 subtype2 subtype3 
  18.050   38.005   23.310 
[1] "11.3 - 37.1 (18.1)"  "18.1 - 121.2 (38.0)" "10.2 - 57.5 (23.3)" 
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype3"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype3"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype3"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       0        2        1
  subtype2       3        0        1
  subtype3       0        0        2
D3V3, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        4        2 
[1] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
          vv
clus       T1+T2+T4
  subtype1        3
  subtype2        4
  subtype3        2
[1] "NOT AVAILABLE: table dimension [3x1]"
D3V5, binary
          cls
clus       0 1
  subtype1 3 0
  subtype2 1 3
  subtype3 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    1    3
  subtype3    1    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        1        1
  MALE          0        3        2

Clustering(4) Variable = MIRSEQ_CNMF
D4V1, survival
          sevent
clus2      0 1
  subtype1 3 1
  subtype3 3 1
subtype1 subtype3 
       4        4 
subtype1 subtype3 
       1        1 
$subtype1
TCGA-OR-A5JJ TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       10.16        37.15        11.31        23.31 

$subtype3
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR 
       57.53        46.78        29.23       121.25 

subtype1 subtype3 
   10.16    29.23 
subtype1 subtype3 
   37.15   121.25 
subtype1 subtype3 
  17.310   52.155 
[1] "10.2 - 37.1 (17.3)"  "29.2 - 121.2 (52.2)"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "hr="     "2.2e+09"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       0        2        2
  subtype3       3        0        0
D4V3, multiclass
          vv
clus       T1+T2+T4
  subtype1        4
  subtype3        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D4V5, binary
          cls
clus       0 1
  subtype1 3 1
  subtype3 1 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype3    1    3
        clus
vv       subtype1 subtype3
  FEMALE        3        1
  MALE          1        3

Clustering(5) Variable = MIRSEQ_CHIERARCHICAL
D5V1, survival
          sevent
clus2      0 1
  subtype1 1 2
  subtype2 2 1
  subtype3 3 1
subtype1 subtype2 subtype3 
       3        3        4 
subtype1 subtype2 subtype3 
       2        1        1 
$subtype1
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JR 
       18.08        18.05       121.25 

$subtype2
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO 
       57.53        46.78        29.23 

$subtype3
TCGA-OR-A5JJ TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       10.16        37.15        11.31        23.31 

subtype1 subtype2 subtype3 
   18.05    29.23    10.16 
subtype1 subtype2 subtype3 
  121.25    57.53    37.15 
subtype1 subtype2 subtype3 
   18.08    46.78    17.31 
[1] "18.1 - 121.2 (18.1)" "29.2 - 57.5 (46.8)"  "10.2 - 37.1 (17.3)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       1        0        2
  subtype2       2        0        0
  subtype3       0        2        2
D5V3, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       3        2        4 
[1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
          vv
clus       T1+T2+T4
  subtype1        3
  subtype2        2
  subtype3        4
[1] "NOT AVAILABLE: table dimension [3x1]"
D5V5, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 1 2
  subtype3 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    1    2
  subtype3    3    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        1        3
  MALE          2        2        1

Clustering(6) Variable = MIRSEQ_MATURE_CNMF
D6V1, survival
          sevent
clus2      0 1
  subtype1 3 1
  subtype3 3 1
subtype1 subtype3 
       4        4 
subtype1 subtype3 
       1        1 
$subtype1
TCGA-OR-A5JJ TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       10.16        37.15        11.31        23.31 

$subtype3
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR 
       57.53        46.78        29.23       121.25 

subtype1 subtype3 
   10.16    29.23 
subtype1 subtype3 
   37.15   121.25 
subtype1 subtype3 
  17.310   52.155 
[1] "10.2 - 37.1 (17.3)"  "29.2 - 121.2 (52.2)"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[8] "subtype1"
[1] "hr="     "2.2e+09"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       0        2        2
  subtype3       3        0        0
D6V3, multiclass
          vv
clus       T1+T2+T4
  subtype1        4
  subtype3        3
[1] "NOT AVAILABLE: table dimension [2x1]"
D6V5, binary
          cls
clus       0 1
  subtype1 3 1
  subtype3 1 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype3    1    3
        clus
vv       subtype1 subtype3
  FEMALE        3        1
  MALE          1        3

Clustering(7) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D7V1, survival
          sevent
clus2      0 1
  subtype1 3 1
  subtype2 2 1
  subtype3 1 2
subtype1 subtype2 subtype3 
       4        3        3 
subtype1 subtype2 subtype3 
       1        1        2 
$subtype1
TCGA-OR-A5JJ TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
       10.16        37.15        11.31        23.31 

$subtype2
TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO 
       57.53        46.78        29.23 

$subtype3
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JR 
       18.08        18.05       121.25 

subtype1 subtype2 subtype3 
   10.16    29.23    18.05 
subtype1 subtype2 subtype3 
   37.15    57.53   121.25 
subtype1 subtype2 subtype3 
   17.31    46.78    18.08 
[1] "10.2 - 37.1 (17.3)"  "29.2 - 57.5 (46.8)"  "18.1 - 121.2 (18.1)"
 [1] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1"
 [1] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1"
 [1] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE IV
  subtype1       0        2        2
  subtype2       2        0        0
  subtype3       1        0        2
D7V3, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        2        3 
[1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
          vv
clus       T1+T2+T4
  subtype1        4
  subtype2        2
  subtype3        3
[1] "NOT AVAILABLE: table dimension [3x1]"
D7V5, binary
          cls
clus       0 1
  subtype1 3 1
  subtype2 1 2
  subtype3 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    1    2
  subtype3    1    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        1        1
  MALE          1        2        2
> q(save="no")
