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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/423573/READ-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/READ-TP/3536846/READ-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-TP", "-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=READ-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

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] "data2feature, selection=ALL"
 [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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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"   "MIRSEQ_CNMF"         
[7] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 69 columns, 0 survival variables, and 7 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
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             5
  CLUS_2          16             5
  CLUS_3          17             2
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          18             5
  CLUS_2          22             4
  CLUS_3          12             3
D1V3, multiclass
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             5
  CLUS_2          12             2
  CLUS_3          20             3
D1V5, multiclass
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           1             1
  CLUS_3           3             0
  CLUS_4           6             0
  CLUS_5          45             9
D1V7, 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
D2V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              8
  CLUS_2           11             10
  CLUS_3            8             11
D2V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              7
  CLUS_2            8             18
  CLUS_3           11              4
D2V3, multiclass
D2V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7              9
  CLUS_2            8              6
  CLUS_3           12             11
D2V5, multiclass
D2V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            1              5
  CLUS_5           30             24
D2V7, 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
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             16
  CLUS_2           15              6
  CLUS_3           17              2
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             15
  CLUS_2           20              6
  CLUS_3           12              3
D3V3, multiclass
D3V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              6
  CLUS_2           12              2
  CLUS_3           13             10
D3V5, multiclass
D3V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            5              1
  CLUS_5           34             20
D3V7, 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
                    V1                     V2                     V3 
           "MRNA_CNMF"   "MRNA_CHIERARCHICAL"              "CN_CNMF" 
                    V4                     V5                     V6 
           "RPPA_CNMF"   "RPPA_CHIERARCHICAL"          "MIRSEQ_CNMF" 
                    V7 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
