
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/6369947/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/6159637/KICH-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-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/6159637/KICH-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/6369947/transformed.cor.cli.txt"

nPatients in clinical file=66, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 7 to 6."
[1]  6 66
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
             8             58 
  MUC2 MUTATED MUC2 WILD-TYPE 
             8             58 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             45 
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             45 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
[1] "PRSS3 MUTATION ANALYSIS"
[1] 3
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              7              59 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              7              59 
[1] "HLA-C MUTATION ANALYSIS"
[1] 3
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              59 
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              59 
[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 = MUC2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC2 MUTATED        0      6      2
  MUC2 WILD-TYPE      5     41     12
D1V1, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            0              5
  CLUS_2            6             41
  CLUS_3            2             12
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC2 MUTATED        2      6      0
  MUC2 WILD-TYPE     16     29     13
D1V2, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            2             16
  CLUS_2            6             29
  CLUS_3            0             13
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC2 MUTATED        3      3      2      0
  MUC2 WILD-TYPE     16     19     13     10
D1V3, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            3             16
  CLUS_2            3             19
  CLUS_3            2             13
  CLUS_4            0             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC2 MUTATED        1      0      2      1      4
  MUC2 WILD-TYPE      9     10     15      5     19
D1V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC2 MUTATED        1      4      3
  MUC2 WILD-TYPE     19     20     19
D1V5, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            4             20
  CLUS_3            3             19
D1V6, binary
                cls
clus              0  1
  MUC2 MUTATED    0  8
  MUC2 WILD-TYPE  9 49
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      0    8
  MUC2 WILD-TYPE    9   49
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            8             49
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC2 MUTATED        1      1      4      1      1
  MUC2 WILD-TYPE      9     15     12      9     13
D1V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC2 MUTATED        0      1      3      4
  MUC2 WILD-TYPE     12      7     22     17
D1V8, multiclass
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  CLUS_1            0             12
  CLUS_2            1              7
  CLUS_3            3             22
  CLUS_4            4             17

Clustering(2) Variable = MUC6 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC6 MUTATED        2     12      7
  MUC6 WILD-TYPE      3     35      7
D2V1, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            2              3
  CLUS_2           12             35
  CLUS_3            7              7
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC6 MUTATED        7     11      3
  MUC6 WILD-TYPE     11     24     10
D2V2, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            7             11
  CLUS_2           11             24
  CLUS_3            3             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC6 MUTATED        6     10      4      1
  MUC6 WILD-TYPE     13     12     11      9
D2V3, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            6             13
  CLUS_2           10             12
  CLUS_3            4             11
  CLUS_4            1              9
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC6 MUTATED        2      1      9      2      7
  MUC6 WILD-TYPE      8      9      8      4     16
D2V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MUC6 MUTATED        4     10      7
  MUC6 WILD-TYPE     16     14     15
D2V5, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            4             16
  CLUS_2           10             14
  CLUS_3            7             15
D2V6, binary
                cls
clus              0  1
  MUC6 MUTATED    1 20
  MUC6 WILD-TYPE  8 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      1   20
  MUC6 WILD-TYPE    8   37
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            1              8
  CLUS_2           20             37
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MUC6 MUTATED        6      5      3      4      3
  MUC6 WILD-TYPE      4     11     13      6     11
D2V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC6 MUTATED        1      3      9      8
  MUC6 WILD-TYPE     11      5     16     13
D2V8, multiclass
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  CLUS_1            1             11
  CLUS_2            3              5
  CLUS_3            9             16
  CLUS_4            8             13

Clustering(3) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2     14      6
  TP53 WILD-TYPE      3     33      8
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              3
  CLUS_2           14             33
  CLUS_3            6              8
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3     16      3
  TP53 WILD-TYPE     15     19     10
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             15
  CLUS_2           16             19
  CLUS_3            3             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        6      6      9      1
  TP53 WILD-TYPE     13     16      6      9
D3V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             13
  CLUS_2            6             16
  CLUS_3            9              6
  CLUS_4            1              9
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        7      1      6      2      6
  TP53 WILD-TYPE      3      9     11      4     17
D3V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        5      9      8
  TP53 WILD-TYPE     15     15     14
D3V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             15
  CLUS_2            9             15
  CLUS_3            8             14
D3V6, binary
                cls
clus              0  1
  TP53 MUTATED    2 20
  TP53 WILD-TYPE  7 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2   20
  TP53 WILD-TYPE    7   37
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              7
  CLUS_2           20             37
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        5      5      4      3      5
  TP53 WILD-TYPE      5     11     12      7      9
D3V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        3      3      8      8
  TP53 WILD-TYPE      9      5     17     13
D3V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              9
  CLUS_2            3              5
  CLUS_3            8             17
  CLUS_4            8             13

Clustering(4) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        2      3      1
  PTEN WILD-TYPE      3     44     13
D4V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2              3
  CLUS_2            3             44
  CLUS_3            1             13
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      3      0
  PTEN WILD-TYPE     15     32     13
D4V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             15
  CLUS_2            3             32
  CLUS_3            0             13
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        2      1      3      0
  PTEN WILD-TYPE     17     21     12     10
D4V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             17
  CLUS_2            1             21
  CLUS_3            3             12
  CLUS_4            0             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        3      0      1      0      2
  PTEN WILD-TYPE      7     10     16      6     21
D4V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      4      1
  PTEN WILD-TYPE     19     20     21
D4V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             19
  CLUS_2            4             20
  CLUS_3            1             21
D4V6, binary
                cls
clus              0  1
  PTEN MUTATED    0  6
  PTEN WILD-TYPE  9 51
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    6
  PTEN WILD-TYPE    9   51
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              9
  CLUS_2            6             51
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        4      0      1      0      1
  PTEN WILD-TYPE      6     16     15     10     13
D4V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        0      0      1      5
  PTEN WILD-TYPE     12      8     24     16
D4V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             12
  CLUS_2            0              8
  CLUS_3            1             24
  CLUS_4            5             16

Clustering(5) Variable = PRSS3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRSS3 MUTATED        0      4      3
  PRSS3 WILD-TYPE      5     43     11
D5V1, multiclass
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             4              43
  CLUS_3             3              11
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRSS3 MUTATED        1      4      2
  PRSS3 WILD-TYPE     17     31     11
D5V2, multiclass
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             1              17
  CLUS_2             4              31
  CLUS_3             2              11
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRSS3 MUTATED        0      6      1      0
  PRSS3 WILD-TYPE     19     16     14     10
D5V3, multiclass
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             6              16
  CLUS_3             1              14
  CLUS_4             0              10
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRSS3 MUTATED        1      0      4      1      1
  PRSS3 WILD-TYPE      9     10     13      5     22
D5V4, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRSS3 MUTATED        3      0      4
  PRSS3 WILD-TYPE     17     24     18
D5V5, multiclass
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             0              24
  CLUS_3             4              18
D5V6, binary
                 cls
clus               0  1
  PRSS3 MUTATED    0  7
  PRSS3 WILD-TYPE  9 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      0    7
  PRSS3 WILD-TYPE    9   50
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             7              50
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PRSS3 MUTATED        0      2      1      2      2
  PRSS3 WILD-TYPE     10     14     15      8     12
D5V7, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRSS3 MUTATED        2      1      4      0
  PRSS3 WILD-TYPE     10      7     21     21
D5V8, multiclass
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1               7
  CLUS_3             4              21
  CLUS_4             0              21

Clustering(6) Variable = HLA-C MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        1      4      2
  HLA-C WILD-TYPE      4     43     12
D6V1, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             1               4
  CLUS_2             4              43
  CLUS_3             2              12
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        3      3      1
  HLA-C WILD-TYPE     15     32     12
D6V2, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             3              15
  CLUS_2             3              32
  CLUS_3             1              12
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-C MUTATED        3      3      1      0
  HLA-C WILD-TYPE     16     19     14     10
D6V3, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             3              16
  CLUS_2             3              19
  CLUS_3             1              14
  CLUS_4             0              10
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-C MUTATED        1      0      3      0      3
  HLA-C WILD-TYPE      9     10     14      6     20
D6V4, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        0      3      4
  HLA-C WILD-TYPE     20     21     18
D6V5, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             0              20
  CLUS_2             3              21
  CLUS_3             4              18
D6V6, binary
                 cls
clus               0  1
  HLA-C MUTATED    0  7
  HLA-C WILD-TYPE  9 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      0    7
  HLA-C WILD-TYPE    9   50
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             0               9
  CLUS_2             7              50
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-C MUTATED        1      1      3      2      0
  HLA-C WILD-TYPE      9     15     13      8     14
D6V7, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-C MUTATED        0      1      4      2
  HLA-C WILD-TYPE     12      7     21     19
D6V8, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             0              12
  CLUS_2             1               7
  CLUS_3             4              21
  CLUS_4             2              19
> q(save="no")
