
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/375952/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/DLBC-TP/2907746/1.GDAC_mergedClustering.Finished/DLBC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=DLBC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[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=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=17, in cluster file=18, common to both=17
[1] "Reduce the number of clustering variables from 13 to 9."
[1]  9 17
[1] "Amp Peak 1(2p16.1) mutation analysis"
[1] 3
  AMP PEAK 1(2P16.1) MUTATED AMP PEAK 1(2P16.1) WILD-TYPE 
                           6                           11 
  AMP PEAK 1(2P16.1) MUTATED AMP PEAK 1(2P16.1) WILD-TYPE 
                           6                           11 
[1] "Del Peak  2(1q43) mutation analysis"
[1] 3
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          3                          14 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          3                          14 
[1] "Del Peak  3(2q22.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q22.3) MUTATED DEL PEAK  3(2Q22.3) WILD-TYPE 
                            4                            13 
  DEL PEAK  3(2Q22.3) MUTATED DEL PEAK  3(2Q22.3) WILD-TYPE 
                            4                            13 
[1] "Del Peak  4(6q14.1) mutation analysis"
[1] 3
  DEL PEAK  4(6Q14.1) MUTATED DEL PEAK  4(6Q14.1) WILD-TYPE 
                            4                            13 
  DEL PEAK  4(6Q14.1) MUTATED DEL PEAK  4(6Q14.1) WILD-TYPE 
                            4                            13 
[1] "Del Peak  5(6q23.3) mutation analysis"
[1] 3
  DEL PEAK  5(6Q23.3) MUTATED DEL PEAK  5(6Q23.3) WILD-TYPE 
                            3                            14 
  DEL PEAK  5(6Q23.3) MUTATED DEL PEAK  5(6Q23.3) WILD-TYPE 
                            3                            14 
[1] "Del Peak  7(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                            4                            13 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                            4                            13 
[1] "Del Peak  9(13q33.3) mutation analysis"
[1] 3
  DEL PEAK  9(13Q33.3) MUTATED DEL PEAK  9(13Q33.3) WILD-TYPE 
                             3                             14 
  DEL PEAK  9(13Q33.3) MUTATED DEL PEAK  9(13Q33.3) WILD-TYPE 
                             3                             14 
[1] "Del Peak 10(15q15.1) mutation analysis"
[1] 3
  DEL PEAK 10(15Q15.1) MUTATED DEL PEAK 10(15Q15.1) WILD-TYPE 
                             4                             13 
  DEL PEAK 10(15Q15.1) MUTATED DEL PEAK 10(15Q15.1) WILD-TYPE 
                             4                             13 
[1] "Del Peak 11(16p13.13) mutation analysis"
[1] 3
  DEL PEAK 11(16P13.13) MUTATED DEL PEAK 11(16P13.13) WILD-TYPE 
                              3                              14 
  DEL PEAK 11(16P13.13) MUTATED DEL PEAK 11(16P13.13) WILD-TYPE 
                              3                              14 
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"

Input Data has 1 rows and 17 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 17 columns, 0 survival variables, and 1 non-survival variables.
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(2p16.1) mutation analysis
D1V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P16.1) MUTATED      6    0
  AMP PEAK 1(2P16.1) WILD-TYPE    3    8
        clus
vv       AMP PEAK 1(2P16.1) MUTATED AMP PEAK 1(2P16.1) WILD-TYPE
  CLUS_1                          6                            3
  CLUS_2                          0                            8

Clustering(2) Variable = Del Peak  2(1q43) mutation analysis
D2V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED      3    0
  DEL PEAK  2(1Q43) WILD-TYPE    6    8
        clus
vv       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  CLUS_1                         3                           6
  CLUS_2                         0                           8

Clustering(3) Variable = Del Peak  3(2q22.3) mutation analysis
D3V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.3) MUTATED      2    2
  DEL PEAK  3(2Q22.3) WILD-TYPE    7    6
        clus
vv       DEL PEAK  3(2Q22.3) MUTATED DEL PEAK  3(2Q22.3) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           2                             6

Clustering(4) Variable = Del Peak  4(6q14.1) mutation analysis
D4V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(6Q14.1) MUTATED      2    2
  DEL PEAK  4(6Q14.1) WILD-TYPE    7    6
        clus
vv       DEL PEAK  4(6Q14.1) MUTATED DEL PEAK  4(6Q14.1) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           2                             6

Clustering(5) Variable = Del Peak  5(6q23.3) mutation analysis
D5V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.3) MUTATED      2    1
  DEL PEAK  5(6Q23.3) WILD-TYPE    7    7
        clus
vv       DEL PEAK  5(6Q23.3) MUTATED DEL PEAK  5(6Q23.3) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           1                             7

Clustering(6) Variable = Del Peak  7(9p21.3) mutation analysis
D6V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED      3    1
  DEL PEAK  7(9P21.3) WILD-TYPE    6    7
        clus
vv       DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           1                             7

Clustering(7) Variable = Del Peak  9(13q33.3) mutation analysis
D7V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(13Q33.3) MUTATED      2    1
  DEL PEAK  9(13Q33.3) WILD-TYPE    7    7
        clus
vv       DEL PEAK  9(13Q33.3) MUTATED DEL PEAK  9(13Q33.3) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            1                              7

Clustering(8) Variable = Del Peak 10(15q15.1) mutation analysis
D8V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(15Q15.1) MUTATED      2    2
  DEL PEAK 10(15Q15.1) WILD-TYPE    7    6
        clus
vv       DEL PEAK 10(15Q15.1) MUTATED DEL PEAK 10(15Q15.1) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            2                              6

Clustering(9) Variable = Del Peak 11(16p13.13) mutation analysis
D9V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(16P13.13) MUTATED      3    0
  DEL PEAK 11(16P13.13) WILD-TYPE    6    8
        clus
vv       DEL PEAK 11(16P13.13) MUTATED DEL PEAK 11(16P13.13) WILD-TYPE
  CLUS_1                             3                               6
  CLUS_2                             0                               8
                V1 
"METHLYATION_CNMF" 
> q(save="no")
