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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_mutation_onlysig.3.4048/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/400701/BLCA-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/BLCA-TP/3143259/1.GDAC_mergedClustering.Finished/BLCA-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=BLCA-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=BLCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=153, in cluster file=28, common to both=28
[1]  3 28
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5              23 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5              23 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               24 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               24 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 28 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              5
  CLUS_2            5              9
  CLUS_3            2              2
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            4              7
  CLUS_3            3              0
  CLUS_4            2              6
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            3              3
  CLUS_3            2              5
  CLUS_4            5              3
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6              2
  CLUS_2            2              5
  CLUS_3            3              7
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2              2
  CLUS_3            5              4
  CLUS_4            3              1
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              4
  CLUS_2            1              6
  CLUS_3            6              6
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              5
  CLUS_2            3              4
  CLUS_3            6              8
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            7              6
  CLUS_4            2              6
  CLUS_5            0              1

Clustering(2) Variable = FBXW7 MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             4              10
  CLUS_3             0               4
D2V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             5               6
  CLUS_3             0               3
  CLUS_4             0               8
D2V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             2               4
  CLUS_3             2               5
  CLUS_4             1               7
D2V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             2               5
  CLUS_3             2               8
D2V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1               3
  CLUS_3             2               7
  CLUS_4             1               3
D2V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             0               7
  CLUS_3             4               8
D2V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             1               6
  CLUS_3             2              12
D2V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2               4
  CLUS_2             2              11
  CLUS_4             1               7
  CLUS_5             0               1

Clustering(3) Variable = NFE2L2 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              4               10
  CLUS_3              0                4
D3V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              3                8
  CLUS_3              0                3
  CLUS_4              0                8
D3V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              2                4
  CLUS_3              2                5
  CLUS_4              0                8
D3V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              1                6
  CLUS_3              2                8
D3V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1                3
  CLUS_3              2                7
  CLUS_4              0                4
D3V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              1                6
  CLUS_3              3                9
D3V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              2                5
  CLUS_3              1               13
D3V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                5
  CLUS_2              3               10
  CLUS_4              0                8
  CLUS_5              0                1
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"             "RPPA_CNMF" 
                     V4                      V5                      V6 
   "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
