
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/8282843/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/8282695/KICH-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[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" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/8282695/KICH-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/8282843/transformed.cor.cli.txt"

nPatients in clinical file=66, in cluster file=66, common to both=66
[1]  2 66
[1] "AMP PEAK 1(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
[1] "AMP PEAK 2(15Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 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.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 0 survival variables, and 8 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
MIRSEQ_MATURE_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(8Q11.23) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(8Q11.23) MUTATED        0     16      3
  AMP PEAK 1(8Q11.23) WILD-TYPE      5     31     11
D1V1, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           0                             5
  CLUS_2                          16                            31
  CLUS_3                           3                            11
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(8Q11.23) MUTATED        4     10      5
  AMP PEAK 1(8Q11.23) WILD-TYPE     14     25      8
D1V2, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                          10                            25
  CLUS_3                           5                             8
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 1(8Q11.23) MUTATED        3     13      2      1
  AMP PEAK 1(8Q11.23) WILD-TYPE     16      9     13      9
D1V3, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                          13                             9
  CLUS_3                           2                            13
  CLUS_4                           1                             9
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 1(8Q11.23) MUTATED        2      2     11      0      4
  AMP PEAK 1(8Q11.23) WILD-TYPE      8      8      6      6     19
D1V4, multiclass
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(8Q11.23) MUTATED        6      7      6
  AMP PEAK 1(8Q11.23) WILD-TYPE     14     17     16
D1V5, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           6                            14
  CLUS_2                           7                            17
  CLUS_3                           6                            16
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK 1(8Q11.23) MUTATED    2 17
  AMP PEAK 1(8Q11.23) WILD-TYPE  7 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) MUTATED      2   17
  AMP PEAK 1(8Q11.23) WILD-TYPE    7   40
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                          17                            40
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 1(8Q11.23) MUTATED        3      3      5      3      5
  AMP PEAK 1(8Q11.23) WILD-TYPE      7     13     11      7      9
D1V7, multiclass
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 1(8Q11.23) MUTATED        3      4      8      4
  AMP PEAK 1(8Q11.23) WILD-TYPE      9      4     17     17
D1V8, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           3                             9
  CLUS_2                           4                             4
  CLUS_3                           8                            17
  CLUS_4                           4                            17

Clustering(2) Variable = AMP PEAK 2(15Q22.31) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(15Q22.31) MUTATED        0     15      8
  AMP PEAK 2(15Q22.31) WILD-TYPE      5     32      6
D2V1, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            0                              5
  CLUS_2                           15                             32
  CLUS_3                            8                              6
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(15Q22.31) MUTATED        6     14      3
  AMP PEAK 2(15Q22.31) WILD-TYPE     12     21     10
D2V2, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                           14                             21
  CLUS_3                            3                             10
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 2(15Q22.31) MUTATED        5     13      5      0
  AMP PEAK 2(15Q22.31) WILD-TYPE     14      9     10     10
D2V3, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                           13                              9
  CLUS_3                            5                             10
  CLUS_4                            0                             10
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 2(15Q22.31) MUTATED        4      1     11      1      6
  AMP PEAK 2(15Q22.31) WILD-TYPE      6      9      6      5     17
D2V4, multiclass
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(15Q22.31) MUTATED        5     10      8
  AMP PEAK 2(15Q22.31) WILD-TYPE     15     14     14
D2V5, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             15
  CLUS_2                           10                             14
  CLUS_3                            8                             14
D2V6, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED    1 22
  AMP PEAK 2(15Q22.31) WILD-TYPE  8 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      1   22
  AMP PEAK 2(15Q22.31) WILD-TYPE    8   35
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                           22                             35
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 2(15Q22.31) MUTATED        3      5      7      3      5
  AMP PEAK 2(15Q22.31) WILD-TYPE      7     11      9      7      9
D2V7, multiclass
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 2(15Q22.31) MUTATED        2      3     11      7
  AMP PEAK 2(15Q22.31) WILD-TYPE     10      5     14     14
D2V8, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            2                             10
  CLUS_2                            3                              5
  CLUS_3                           11                             14
  CLUS_4                            7                             14
> q(save="no")
