
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/10441/12/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/ESCA-TP/4428472/ESCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=ESCA-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=ESCA-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/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/ESCA-TP/4428472/ESCA-TP.mergedcluster.txt"

nPatients in clinical file=19, in cluster file=63, common to both=19
[1]  2 19
[1] "CN_CNMF"
[1] 3
1 2 3 
7 3 9 
1 2 3 
7 3 9 
[1] "METHLYATION_CNMF"
[1] 3
1 2 3 
6 4 9 
1 2 3 
6 4 9 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"          "VITALSTATUS"           "DAYSTODEATH"          
 [4] "DAYSTOLASTFOLLOWUP"    "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
 [7] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "DCCUPLOADDATE"        
[10] "GENDER"                "NUMBERPACKYEARSSMOKED" "BATCHNUMBER"          

Input Data has 12 rows and 19 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
          NA           NA           NA            1            8           NA 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
         106          112          124           NA          101           NA 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
          NA          934          882           NA           NA            4 
TCGA-LN-A4A9 
           2 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	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:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 19 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 4  7  6  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4     7     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 4  7  6  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4     7     8 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
 7  9  2  1 
[1] "table(vv)"
vv
      N0 N1+N2+N3 
       7       12 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
 7  9  2  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 7

$Class1_nSamples
[1] 12

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2+N3"


      N0 N1+N2+N3 
       7       12 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 4 0
  subtype2 1 2
  subtype3 5 3
subtype1 subtype2 subtype3 
       4        3        8 
subtype1 subtype2 subtype3 
       0        2        3 
$subtype1
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.03         4.08         0.13         0.07 

$subtype2
TCGA-IG-A4QS TCGA-L5-A4OQ TCGA-L5-A4OW 
        0.26         1.38         7.10 

$subtype3
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS 
        3.48         3.68        18.35         3.32         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OX 
       29.00         7.43 

subtype1 subtype2 subtype3 
    0.03     0.26     3.16 
subtype1 subtype2 subtype3 
    4.08     7.10    30.71 
subtype1 subtype2 subtype3 
   0.100    1.380    5.555 
[1] "0.0 - 4.1 (0.1)"  "0.3 - 7.1 (1.4)"  "3.2 - 30.7 (5.6)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype3" "subtype1" "subtype1"
D1V2, continuous
          vv
clus       STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        1         2         2          2          0          0
  subtype2        0         0         1          1          1          0
  subtype3        1         1         4          1          1          1
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  3     3
  subtype2  0  2     1
  subtype3  3  2     4
D1V4, multiclass
          vv
clus       N0 N1+N2+N3
  subtype1  4        3
  subtype2  0        3
  subtype3  3        6
D1V5, multiclass
          clus
vv         subtype1 subtype2 subtype3
  N0              4        0        3
  N1+N2+N3        3        3        6
D1V6, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 1 2
  subtype3 1 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    1    2
  subtype3    1    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        1        1
  MALE          6        2        8
D1V7, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        2        6 
 [1] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype1"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype2 2 1
  subtype3 5 4
subtype1 subtype2 subtype3 
       3        3        9 
subtype1 subtype2 subtype3 
       0        1        4 
$subtype1
TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        4.08         0.13         0.07 

$subtype2
TCGA-IG-A4P3 TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         1.38        30.71 

$subtype3
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.26         3.48         3.68        18.35         3.32         3.16 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       29.00         7.10         7.43 

subtype1 subtype2 subtype3 
    0.07     0.03     0.26 
subtype1 subtype2 subtype3 
    4.08    30.71    29.00 
subtype1 subtype2 subtype3 
    0.13     1.38     3.68 
[1] "0.1 - 4.1 (0.1)"  "0.0 - 30.7 (1.4)" "0.3 - 29.0 (3.7)"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1"
D2V2, continuous
          vv
clus       STAGE IA STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        1         2         1          2          0          0
  subtype2        0         0         2          2          0          0
  subtype3        1         1         4          0          2          1
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  2     3
  subtype2  0  3     1
  subtype3  3  2     4
D2V4, multiclass
          vv
clus       N0 N1+N2+N3
  subtype1  4        2
  subtype2  1        3
  subtype3  2        7
D2V5, multiclass
          clus
vv         subtype1 subtype2 subtype3
  N0              4        1        2
  N1+N2+N3        2        3        7
D2V6, binary
          cls
clus       0 1
  subtype1 1 5
  subtype2 1 3
  subtype3 1 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype2    1    3
  subtype3    1    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        1        1
  MALE          5        3        8
D2V7, continuous
> q(save="no")
