
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_Correlate_Genomic_Events_Preprocess/PCPG-TP/8278445/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/8143061/PCPG-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=PCPG-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-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=PCPG-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/8143061/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/8278445/transformed.cor.cli.txt"

nPatients in clinical file=10, in cluster file=159, common to both=9
[1] "Reduce the number of clustering variables from 27 to 10."
[1] 10  9
[1] "AMP PEAK 4(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(14Q24.3) MUTATED AMP PEAK 4(14Q24.3) WILD-TYPE 
                            4                             5 
  AMP PEAK 4(14Q24.3) MUTATED AMP PEAK 4(14Q24.3) WILD-TYPE 
                            4                             5 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             6                              3 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             6                              3 
[1] "DEL PEAK  4(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P24.1) MUTATED DEL PEAK  4(3P24.1) WILD-TYPE 
                            4                             5 
  DEL PEAK  4(3P24.1) MUTATED DEL PEAK  4(3P24.1) WILD-TYPE 
                            4                             5 
[1] "DEL PEAK  5(3Q26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q26.1) MUTATED DEL PEAK  5(3Q26.1) WILD-TYPE 
                            6                             3 
  DEL PEAK  5(3Q26.1) MUTATED DEL PEAK  5(3Q26.1) WILD-TYPE 
                            6                             3 
[1] "DEL PEAK 15(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                             3                              6 
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                             3                              6 
[1] "DEL PEAK 18(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                             4                              5 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                             4                              5 
[1] "DEL PEAK 19(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                             3                              6 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                             3                              6 
[1] "DEL PEAK 20(22Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(22Q12.3) MUTATED DEL PEAK 20(22Q12.3) WILD-TYPE 
                             5                              4 
  DEL PEAK 20(22Q12.3) MUTATED DEL PEAK 20(22Q12.3) WILD-TYPE 
                             5                              4 
[1] "DEL PEAK 21(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                              5                               4 
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                              5                               4 
[1] "DEL PEAK 22(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                            5                             4 
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                            5                             4 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "YEARSTOBIRTH"       "VITALSTATUS"        "DAYSTODEATH"       
[4] "DAYSTOLASTFOLLOWUP" "DCCUPLOADDATE"      "GENDER"            
[7] "RADIATIONTHERAPY"   "BATCHNUMBER"       

Input Data has 8 rows and 9 columns.

[1] "Batch" "8"    
[1] "Last Follow UP"
TCGA-PR-A5PG TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1094          773          211           55           22          766 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
          70          134           24 
Variable 1:'AGE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'BATCH.NUMBER':	nDistinctValues=1,	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 9 columns, 0 survival variables, and 2 non-survival variables.
AGE, nv=8, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 4(14Q24.3) MUTATION ANALYSIS
D1V1, continuous
D1V2, binary
                               cls
clus                            0 1
  AMP PEAK 4(14Q24.3) MUTATED   3 1
  AMP PEAK 4(14Q24.3) WILD-TYPE 3 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(14Q24.3) MUTATED      3    1
  AMP PEAK 4(14Q24.3) WILD-TYPE    3    2
        clus
vv       AMP PEAK 4(14Q24.3) MUTATED AMP PEAK 4(14Q24.3) WILD-TYPE
  FEMALE                           3                             3
  MALE                             1                             2

Clustering(2) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D2V1, continuous
D2V2, binary
                                cls
clus                             0 1
  DEL PEAK  1(1P36.32) MUTATED   4 2
  DEL PEAK  1(1P36.32) WILD-TYPE 2 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      4    2
  DEL PEAK  1(1P36.32) WILD-TYPE    2    1
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            4                              2
  MALE                              2                              1

Clustering(3) Variable = DEL PEAK  4(3P24.1) MUTATION ANALYSIS
D3V1, continuous
D3V2, binary
                               cls
clus                            0 1
  DEL PEAK  4(3P24.1) MUTATED   3 1
  DEL PEAK  4(3P24.1) WILD-TYPE 3 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.1) MUTATED      3    1
  DEL PEAK  4(3P24.1) WILD-TYPE    3    2
        clus
vv       DEL PEAK  4(3P24.1) MUTATED DEL PEAK  4(3P24.1) WILD-TYPE
  FEMALE                           3                             3
  MALE                             1                             2

Clustering(4) Variable = DEL PEAK  5(3Q26.1) MUTATION ANALYSIS
D4V1, continuous
D4V2, binary
                               cls
clus                            0 1
  DEL PEAK  5(3Q26.1) MUTATED   5 1
  DEL PEAK  5(3Q26.1) WILD-TYPE 1 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3Q26.1) MUTATED      5    1
  DEL PEAK  5(3Q26.1) WILD-TYPE    1    2
        clus
vv       DEL PEAK  5(3Q26.1) MUTATED DEL PEAK  5(3Q26.1) WILD-TYPE
  FEMALE                           5                             1
  MALE                             1                             2

Clustering(5) Variable = DEL PEAK 15(11Q22.1) MUTATION ANALYSIS
D5V1, continuous
D5V2, binary
                                cls
clus                             0 1
  DEL PEAK 15(11Q22.1) MUTATED   1 2
  DEL PEAK 15(11Q22.1) WILD-TYPE 5 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q22.1) MUTATED      1    2
  DEL PEAK 15(11Q22.1) WILD-TYPE    5    1
        clus
vv       DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE
  FEMALE                            1                              5
  MALE                              2                              1

Clustering(6) Variable = DEL PEAK 18(17P13.2) MUTATION ANALYSIS
D6V1, continuous
D6V2, binary
                                cls
clus                             0 1
  DEL PEAK 18(17P13.2) MUTATED   3 1
  DEL PEAK 18(17P13.2) WILD-TYPE 3 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17P13.2) MUTATED      3    1
  DEL PEAK 18(17P13.2) WILD-TYPE    3    2
        clus
vv       DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE
  FEMALE                            3                              3
  MALE                              1                              2

Clustering(7) Variable = DEL PEAK 19(17Q11.2) MUTATION ANALYSIS
D7V1, continuous
D7V2, binary
                                cls
clus                             0 1
  DEL PEAK 19(17Q11.2) MUTATED   2 1
  DEL PEAK 19(17Q11.2) WILD-TYPE 4 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17Q11.2) MUTATED      2    1
  DEL PEAK 19(17Q11.2) WILD-TYPE    4    2
        clus
vv       DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE
  FEMALE                            2                              4
  MALE                              1                              2

Clustering(8) Variable = DEL PEAK 20(22Q12.3) MUTATION ANALYSIS
D8V1, continuous
D8V2, binary
                                cls
clus                             0 1
  DEL PEAK 20(22Q12.3) MUTATED   4 1
  DEL PEAK 20(22Q12.3) WILD-TYPE 2 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(22Q12.3) MUTATED      4    1
  DEL PEAK 20(22Q12.3) WILD-TYPE    2    2
        clus
vv       DEL PEAK 20(22Q12.3) MUTATED DEL PEAK 20(22Q12.3) WILD-TYPE
  FEMALE                            4                              2
  MALE                              1                              2

Clustering(9) Variable = DEL PEAK 21(22Q13.31) MUTATION ANALYSIS
D9V1, continuous
D9V2, binary
                                 cls
clus                              0 1
  DEL PEAK 21(22Q13.31) MUTATED   3 2
  DEL PEAK 21(22Q13.31) WILD-TYPE 3 1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(22Q13.31) MUTATED      3    2
  DEL PEAK 21(22Q13.31) WILD-TYPE    3    1
        clus
vv       DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE
  FEMALE                             3                               3
  MALE                               2                               1

Clustering(10) Variable = DEL PEAK 22(XP21.1) MUTATION ANALYSIS
D10V1, continuous
D10V2, binary
                               cls
clus                            0 1
  DEL PEAK 22(XP21.1) MUTATED   4 1
  DEL PEAK 22(XP21.1) WILD-TYPE 2 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(XP21.1) MUTATED      4    1
  DEL PEAK 22(XP21.1) WILD-TYPE    2    2
        clus
vv       DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE
  FEMALE                           4                             2
  MALE                             1                             2
> q(save="no")
