
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/READ-TP/6068734/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/6159710/READ-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=READ-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=READ-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/READ-TP/6159710/READ-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/6068734/transformed.cor.cli.txt"

nPatients in clinical file=166, in cluster file=69, common to both=69
[1]  3 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           57            12 
  APC MUTATED APC WILD-TYPE 
           57            12 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 69 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[7] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 69 columns, 0 survival variables, and 9 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       19     16     17
  APC WILD-TYPE      5      5      2
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             5
  CLUS_2          16             5
  CLUS_3          17             2
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       18     22     12
  APC WILD-TYPE      5      4      3
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          18             5
  CLUS_2          22             4
  CLUS_3          12             3
               vv
clus            CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APC MUTATED       11     16     15      9      5
  APC WILD-TYPE      6      2      2      2      0
D1V3, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       11     12     20
  APC WILD-TYPE      5      2      3
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             5
  CLUS_2          12             2
  CLUS_3          20             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED        1      3     11     16     12
  APC WILD-TYPE      1      1      1      5      2
D1V5, multiclass
D1V6, binary
               cls
clus             0  1
  APC MUTATED    5 51
  APC WILD-TYPE  1 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      5   51
  APC WILD-TYPE    1   10
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_2           5             1
  CLUS_3          51            10
               vv
clus            CLUS_1 CLUS_2 CLUS_4
  APC MUTATED       53      2      1
  APC WILD-TYPE      9      2      0
D1V7, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          53             9
  CLUS_2           2             2
  CLUS_4           1             0
               vv
clus            CLUS_1 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED        1      3      6     45
  APC WILD-TYPE      1      0      0      9
D1V8, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           1             1
  CLUS_3           3             0
  CLUS_4           6             0
  CLUS_5          45             9
D1V9, binary
               cls
clus             0  1
  APC MUTATED    4 51
  APC WILD-TYPE  0 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      4   51
  APC WILD-TYPE    0   10
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           4             0
  CLUS_2          51            10

Clustering(2) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       16     11      8
  KRAS WILD-TYPE      8     10     11
D2V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              8
  CLUS_2           11             10
  CLUS_3            8             11
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED       16      8     11
  KRAS WILD-TYPE      7     18      4
D2V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              7
  CLUS_2            8             18
  CLUS_3           11              4
                vv
clus             CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        3     13      9      8      5
  KRAS WILD-TYPE     14      5      8      3      0
D2V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KRAS MUTATED        7      8     12
  KRAS WILD-TYPE      9      6     11
D2V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7              9
  CLUS_2            8              6
  CLUS_3           12             11
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        1      2      6      9      9
  KRAS WILD-TYPE      1      2      6     12      5
D2V5, multiclass
D2V6, binary
                cls
clus              0  1
  KRAS MUTATED    6 30
  KRAS WILD-TYPE  0 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6   30
  KRAS WILD-TYPE    0   31
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_2            6              0
  CLUS_3           30             31
                vv
clus             CLUS_1 CLUS_2 CLUS_4
  KRAS MUTATED       33      2      1
  KRAS WILD-TYPE     29      2      0
D2V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           33             29
  CLUS_2            2              2
  CLUS_4            1              0
                vv
clus             CLUS_1 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        1      2      1     30
  KRAS WILD-TYPE      1      1      5     24
D2V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            1              5
  CLUS_5           30             24
D2V9, binary
                cls
clus              0  1
  KRAS MUTATED    0 34
  KRAS WILD-TYPE  4 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   34
  KRAS WILD-TYPE    4   27
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              4
  CLUS_2           34             27

Clustering(3) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8     15     17
  TP53 WILD-TYPE     16      6      2
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             16
  CLUS_2           15              6
  CLUS_3           17              2
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8     20     12
  TP53 WILD-TYPE     15      6      3
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             15
  CLUS_2           20              6
  CLUS_3           12              3
                vv
clus             CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED       13      9     10      9      3
  TP53 WILD-TYPE      4      9      7      2      2
D3V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       10     12     13
  TP53 WILD-TYPE      6      2     10
D3V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              6
  CLUS_2           12              2
  CLUS_3           13             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        1      3     10     12      9
  TP53 WILD-TYPE      1      1      2      9      5
D3V5, multiclass
D3V6, binary
                cls
clus              0  1
  TP53 MUTATED    2 41
  TP53 WILD-TYPE  4 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2   41
  TP53 WILD-TYPE    4   20
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_2            2              4
  CLUS_3           41             20
                vv
clus             CLUS_1 CLUS_2 CLUS_4
  TP53 MUTATED       40      2      1
  TP53 WILD-TYPE     22      2      0
D3V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           40             22
  CLUS_2            2              2
  CLUS_4            1              0
                vv
clus             CLUS_1 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        1      2      5     34
  TP53 WILD-TYPE      1      1      1     20
D3V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            5              1
  CLUS_5           34             20
D3V9, binary
                cls
clus              0  1
  TP53 MUTATED    4 38
  TP53 WILD-TYPE  0 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   38
  TP53 WILD-TYPE    0   23
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4              0
  CLUS_2           38             23
> q(save="no")
