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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/444816/THCA-HistologicalType_Follicular.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/THCA-HistologicalType_Follicular/3840279/THCA-HistologicalType_Follicular.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=THCA-HistologicalType_Follicular", "-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"                                 
[2] "-oT=THCA-HistologicalType_Follicular"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=99, in cluster file=83, common to both=83
[1]  3 83
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            19             64 
  NRAS MUTATED NRAS WILD-TYPE 
            19             64 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            13             70 
  BRAF MUTATED BRAF WILD-TYPE 
            13             70 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             8             75 
  HRAS MUTATED HRAS WILD-TYPE 
             8             75 
[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 83 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	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=2,	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 83 columns, 0 survival variables, and 9 non-survival variables.
METHLYATION_CNMF, nv=8, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NRAS MUTATION ANALYSIS
D1V1, multiclass
D1V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             18
  CLUS_2            2             14
  CLUS_3            4             11
D1V3, binary
                cls
clus              0  1
  NRAS MUTATED    5  4
  NRAS WILD-TYPE 13 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    4
  NRAS WILD-TYPE   13   30
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             13
  CLUS_2            4             30
D1V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           11             10
  CLUS_2            2             15
  CLUS_3            1             21
  CLUS_4            5             18
D1V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             15
  CLUS_2            0             18
  CLUS_3            6             19
  CLUS_4           13             12
D1V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           11             27
  CLUS_2            4             21
  CLUS_3            4             16
D1V7, binary
                cls
clus              0  1
  NRAS MUTATED    0 19
  NRAS WILD-TYPE 17 47
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   19
  NRAS WILD-TYPE   17   47
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             17
  CLUS_2           19             47
D1V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            8             15
  CLUS_2            3             15
  CLUS_3            7             18
  CLUS_4            1             16
D1V9, binary
                cls
clus              0  1
  NRAS MUTATED   11  8
  NRAS WILD-TYPE 37 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     11    8
  NRAS WILD-TYPE   37   27
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           11             37
  CLUS_2            8             27

Clustering(2) Variable = BRAF MUTATION ANALYSIS
D2V1, multiclass
D2V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             18
  CLUS_2            3             13
  CLUS_3            2             13
D2V3, binary
                cls
clus              0  1
  BRAF MUTATED    2  6
  BRAF WILD-TYPE 16 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    6
  BRAF WILD-TYPE   16   28
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             16
  CLUS_2            6             28
D2V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             20
  CLUS_2            0             17
  CLUS_3           12             10
  CLUS_4            0             23
D2V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             15
  CLUS_2           12              6
  CLUS_3            0             25
  CLUS_4            1             24
D2V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             38
  CLUS_2            4             21
  CLUS_3            9             11
D2V7, binary
                cls
clus              0  1
  BRAF MUTATED   10  3
  BRAF WILD-TYPE  7 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10    3
  BRAF WILD-TYPE    7   63
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           10              7
  CLUS_2            3             63
D2V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             22
  CLUS_2            3             15
  CLUS_3            1             24
  CLUS_4            8              9
D2V9, binary
                cls
clus              0  1
  BRAF MUTATED    1 12
  BRAF WILD-TYPE 47 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   12
  BRAF WILD-TYPE   47   23
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             47
  CLUS_2           12             23

Clustering(3) Variable = HRAS MUTATION ANALYSIS
D3V1, multiclass
D3V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             20
  CLUS_2            5             11
  CLUS_3            1             14
D3V3, binary
                cls
clus              0  1
  HRAS MUTATED    1  6
  HRAS WILD-TYPE 17 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1    6
  HRAS WILD-TYPE   17   28
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             17
  CLUS_2            6             28
D3V4, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            6             15
  CLUS_2            0             17
  CLUS_3            1             21
  CLUS_4            1             22
D3V5, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             15
  CLUS_2            0             18
  CLUS_3            0             25
  CLUS_4            8             17
D3V6, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            7             31
  CLUS_2            0             25
  CLUS_3            1             19
D3V7, binary
                cls
clus              0  1
  HRAS MUTATED    1  7
  HRAS WILD-TYPE 16 59
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1    7
  HRAS WILD-TYPE   16   59
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             16
  CLUS_2            7             59
D3V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            5             18
  CLUS_2            0             18
  CLUS_3            2             23
  CLUS_4            1             16
D3V9, binary
                cls
clus              0  1
  HRAS MUTATED    1  7
  HRAS WILD-TYPE 47 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1    7
  HRAS WILD-TYPE   47   28
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             47
  CLUS_2            7             28
                           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")
