
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/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/423463/CESC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/CESC-TP/3586858/CESC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC-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=CESC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=134, in cluster file=39, common to both=39
[1] "Reduce the number of clustering variables from 7 to 5."
[1]  5 39
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               30 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               30 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              4              35 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              4              35 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              34 
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              34 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               36 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               36 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              3              36 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              3              36 
[1] "data2feature, selection=ALL"
[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 39 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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	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 39 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=3, 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
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PIK3CA MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               12
  CLUS_2              0                7
  CLUS_3              6                8
D1V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               14
  CLUS_2              6               10
  CLUS_3              1                6
D1V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               14
  CLUS_2              1                8
  CLUS_3              1                7
D1V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_2              7               18
  CLUS_3              1                8
D1V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               11
  CLUS_2              2               10
  CLUS_3              0                2
  CLUS_4              3                7
D1V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED    6  3
  PIK3CA WILD-TYPE 23  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      6    3
  PIK3CA WILD-TYPE   23    7
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               23
  CLUS_2              3                7
D1V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               16
  CLUS_2              2                7
  CLUS_3              2                7
D1V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                5
  CLUS_2              0                9
  CLUS_3              8               16

Clustering(2) Variable = TMCC1 MUTATION ANALYSIS
D2V1, multiclass
[1] "Remove cluster labels:" "TMCC1 MUTATED"         
clus
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              2              34 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1M5 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1M6      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-EA-A1QT      TCGA-EX-A1H5 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
D2V2, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2              14
  CLUS_3             0               7
D2V3, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2               7
  CLUS_3             0               8
D2V4, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             2              23
  CLUS_3             0               9
D2V5, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2              10
  CLUS_3             0               2
  CLUS_4             0              10
D2V6, binary
                 cls
clus               0  1
  TMCC1 MUTATED    4  0
  TMCC1 WILD-TYPE 25 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      4    0
  TMCC1 WILD-TYPE   25   10
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             4              25
  CLUS_2             0              10
D2V7, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             1               8
  CLUS_3             0               9
D2V8, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               8
  CLUS_3             3              21

Clustering(3) Variable = CDC27 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             1               6
  CLUS_3             0              14
D3V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              12
  CLUS_2             1              15
  CLUS_3             0               7
D3V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             3               6
  CLUS_3             0               8
D3V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             3              22
  CLUS_3             0               9
D3V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             3               9
  CLUS_3             0               2
  CLUS_4             0              10
D3V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    5  0
  CDC27 WILD-TYPE 24 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      5    0
  CDC27 WILD-TYPE   24   10
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             5              24
  CLUS_2             0              10
D3V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             2               7
  CLUS_3             0               9
D3V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3               6
  CLUS_3             2              22

Clustering(4) Variable = UGT3A2 MUTATION ANALYSIS
D4V1, multiclass
[1] "Remove cluster labels:" "UGT3A2 MUTATED"        
clus
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               1               35 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BL       TCGA-C5-A1BM       TCGA-C5-A1BN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1M6       TCGA-C5-A1M7       TCGA-C5-A1M8 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MK       TCGA-C5-A1ML 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A1MP       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VN       TCGA-EA-A1QT 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A23K       TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
D4V2, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               15
  CLUS_3              0                7
D4V3, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              3                6
  CLUS_3              0                8
D4V4, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2                2
  CLUS_2              1               24
  CLUS_3              0                9
D4V5, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              2               10
  CLUS_3              0                2
  CLUS_4              0               10
D4V6, binary
                  cls
clus                0  1
  UGT3A2 MUTATED    3  0
  UGT3A2 WILD-TYPE 26 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      3    0
  UGT3A2 WILD-TYPE   26   10
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              3               26
  CLUS_2              0               10
D4V7, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              1                8
  CLUS_3              0                9
D4V8, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                7
  CLUS_3              1               23

Clustering(5) Variable = MAPK1 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             0               7
  CLUS_3             3              11
D5V2, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             0               7
D5V3, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0               9
  CLUS_3             0               8
D5V4, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             3              22
  CLUS_3             0               9
D5V5, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             3               9
  CLUS_3             0               2
  CLUS_4             0              10
D5V6, binary
                 cls
clus               0  1
  MAPK1 MUTATED    3  0
  MAPK1 WILD-TYPE 26 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK1 MUTATED      3    0
  MAPK1 WILD-TYPE   26   10
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              26
  CLUS_2             0              10
D5V7, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0               9
  CLUS_3             0               9
D5V8, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               8
  CLUS_3             2              22
                           V1                            V2 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V3                            V4 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V5                            V6 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V7                            V8 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
