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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/444871/THCA-Mut_RAS.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/THCA-Mut_RAS/3818743/THCA-Mut_RAS.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=THCA-Mut_RAS", "-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=THCA-Mut_RAS"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=51, in cluster file=51, common to both=51
[1]  2 51
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            34             17 
  NRAS MUTATED NRAS WILD-TYPE 
            34             17 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14             37 
  HRAS MUTATED HRAS WILD-TYPE 
            14             37 
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"            "RPPA_CNMF"                  
[3] "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF"               
[5] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[7] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[9] "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 9 rows and 51 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"            "RPPA_CNMF"                  
[3] "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF"               
[5] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[7] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[9] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 51 columns, 0 survival variables, and 9 non-survival variables.
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NRAS MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           12              4
  CLUS_2           15             12
  CLUS_3            7              1
D1V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4              1
  CLUS_2            4              2
  CLUS_3            5              2
  CLUS_4            1              7
D1V3, binary
                cls
clus             0 1
  NRAS MUTATED   6 8
  NRAS WILD-TYPE 8 4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      6    8
  NRAS WILD-TYPE    8    4
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            6              8
  CLUS_2            8              4
D1V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           13             10
  CLUS_2           10              4
  CLUS_3           11              3
D1V5, binary
                cls
clus              0  1
  NRAS MUTATED   14 20
  NRAS WILD-TYPE 11  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     14   20
  NRAS WILD-TYPE   11    6
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           14             11
  CLUS_2           20              6
D1V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           11              7
  CLUS_2           10              5
  CLUS_3           13              5
D1V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4              3
  CLUS_2            5              2
  CLUS_3           12              8
  CLUS_4           13              4
D1V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            8              5
  CLUS_2            7              3
  CLUS_3           11              3
  CLUS_4            8              6
D1V9, multiclass

Clustering(2) Variable = HRAS MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            2             14
  CLUS_2           12             15
  CLUS_3            0              8
D2V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1              4
  CLUS_2            2              4
  CLUS_3            1              6
  CLUS_4            6              2
D2V3, binary
                cls
clus             0 1
  HRAS MUTATED   7 3
  HRAS WILD-TYPE 7 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7    3
  HRAS WILD-TYPE    7    9
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            7              7
  CLUS_2            3              9
D2V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1           10             13
  CLUS_2            3             11
  CLUS_3            1             13
D2V5, binary
                cls
clus              0  1
  HRAS MUTATED    9  5
  HRAS WILD-TYPE 16 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      9    5
  HRAS WILD-TYPE   16   21
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            9             16
  CLUS_2            5             21
D2V6, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            7             11
  CLUS_2            4             11
  CLUS_3            3             15
D2V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            3              4
  CLUS_2            1              6
  CLUS_3            7             13
  CLUS_4            3             14
D2V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            3             10
  CLUS_2            3              7
  CLUS_3            3             11
  CLUS_4            5              9
D2V9, multiclass
                           V1                            V2 
           "METHLYATION_CNMF"                   "RPPA_CNMF" 
                           V3                            V4 
         "RPPA_CHIERARCHICAL"                "MRNASEQ_CNMF" 
                           V5                            V6 
      "MRNASEQ_CHIERARCHICAL"                 "MIRSEQ_CNMF" 
                           V7                            V8 
       "MIRSEQ_CHIERARCHICAL"          "MIRSEQ_MATURE_CNMF" 
                           V9 
"MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
