
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.4.4139/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.4.4139/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/411549/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KICH-TP/3144352/1.GDAC_mergedClustering.Finished/KICH-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-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=KICH-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=66, in cluster file=66, common to both=66
[1]  2 66
[1] "Amp Peak 1(8q11.23)"
[1] 3
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                           18                            48 
      AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE 
                           18                            48 
[1] "Amp Peak 2(15q22.31)"
[1] 3
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                            22                             44 
      AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE 
                            22                             44 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 66 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(8q11.23)
D1V1, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                       0                             5
  CLUS_2                      16                            31
  CLUS_3                       2                            12
D1V2, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                       2                            15
  CLUS_2                       9                            25
  CLUS_3                       7                             7
D1V3, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                       3                            16
  CLUS_2                      12                            10
  CLUS_3                       2                            13
  CLUS_4                       1                             9
D1V4, multiclass
D1V5, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                       6                            14
  CLUS_2                       6                            18
  CLUS_3                       6                            16
D1V6, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) CNV         16    2
  AMP PEAK 1(8Q11.23) WILD-TYPE   41    7
        clus
vv       AMP PEAK 1(8Q11.23) CNV AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                      16                            41

Clustering(2) Variable = Amp Peak 2(15q22.31)
D2V1, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                        0                              5
  CLUS_2                       15                             32
  CLUS_3                        7                              7
D2V2, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                        5                             12
  CLUS_2                       12                             22
  CLUS_3                        5                              9
D2V3, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                        5                             14
  CLUS_2                       13                              9
  CLUS_3                        4                             11
  CLUS_4                        0                             10
D2V4, multiclass
D2V5, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                        5                             15
  CLUS_2                        9                             15
  CLUS_3                        8                             14
D2V6, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) CNV         21    1
  AMP PEAK 2(15Q22.31) WILD-TYPE   36    8
        clus
vv       AMP PEAK 2(15Q22.31) CNV AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                       21                             36
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
