
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_Clinical_Clusters_onlysig.81.4078/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/347522/PRAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PRAD-TP/2589023/1.GDAC_clinicalDataPicker.Finished/PRAD-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-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="
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=148, in cluster file=83, common to both=83
[1] 13 83
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5               78 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5               78 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             78 
  TP53 MUTATED TP53 WILD-TYPE 
             5             78 
[1] "FRG1 MUTATION ANALYSIS"
[1] 3
  FRG1 MUTATED FRG1 WILD-TYPE 
             4             79 
  FRG1 MUTATED FRG1 WILD-TYPE 
             4             79 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
             4             79 
  SPOP MUTATED SPOP WILD-TYPE 
             4             79 
[1] "YBX1 MUTATION ANALYSIS"
[1] 3
  YBX1 MUTATED YBX1 WILD-TYPE 
             3             80 
  YBX1 MUTATED YBX1 WILD-TYPE 
             3             80 
[1] "CCNF MUTATION ANALYSIS"
[1] 3
  CCNF MUTATED CCNF WILD-TYPE 
             3             80 
  CCNF MUTATED CCNF WILD-TYPE 
             3             80 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3               80 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3               80 
[1] "PRR21 MUTATION ANALYSIS"
[1] 3
  PRR21 MUTATED PRR21 WILD-TYPE 
              4              79 
  PRR21 MUTATED PRR21 WILD-TYPE 
              4              79 
[1] "AGT MUTATION ANALYSIS"
[1] 3
  AGT MUTATED AGT WILD-TYPE 
            3            80 
  AGT MUTATED AGT WILD-TYPE 
            3            80 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               80 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               80 
[1] "DUSP27 MUTATION ANALYSIS"
[1] 3
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               3               80 
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               3               80 
[1] "OR4D5 MUTATION ANALYSIS"
[1] 3
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              3              80 
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              3              80 
[1] "OR6N1 MUTATION ANALYSIS"
[1] 3
  OR6N1 MUTATED OR6N1 WILD-TYPE 
              3              80 
  OR6N1 MUTATED OR6N1 WILD-TYPE 
              3              80 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 83 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          424 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
          60           91          731           31          395         1065 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
         942           31           62           28         1339          365 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
          31          700           31          458          731           62 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
         395          485          820          303          974         1004 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
          91          881          378          605          594          396 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
         536          532          729          244          530          229 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
         447          356          182          907         1096          737 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
         788          782          724         1061          783          849 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
        1195         1153          842         1403          834          790 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
         567          397         1272          724          910          519 
TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6348 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 
        2328         1669         1144         1000          822          993 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
         841          804          875          806          846          505 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
         664          390          356         1442         1014 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 83 columns, 0 survival variables, and 2 non-survival variables.
AGE, nv=27, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NKX3-1 MUTATION ANALYSIS
D1V1, continuous
D1V2, binary
                  cls
clus                0  1
  NKX3-1 MUTATED    0  5
  NKX3-1 WILD-TYPE  5 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      0    5
  NKX3-1 WILD-TYPE    5   73
     clus
vv    NKX3-1 MUTATED NKX3-1 WILD-TYPE
  NO               0                5
  YES              5               73

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, continuous
D2V2, binary
                cls
clus              0  1
  TP53 MUTATED    0  5
  TP53 WILD-TYPE  5 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    5
  TP53 WILD-TYPE    5   73
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             0              5
  YES            5             73

Clustering(3) Variable = FRG1 MUTATION ANALYSIS
D3V1, continuous
D3V2, binary
                cls
clus              0  1
  FRG1 MUTATED    1  3
  FRG1 WILD-TYPE  4 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      1    3
  FRG1 WILD-TYPE    4   75
     clus
vv    FRG1 MUTATED FRG1 WILD-TYPE
  NO             1              4
  YES            3             75

Clustering(4) Variable = SPOP MUTATION ANALYSIS
D4V1, continuous
D4V2, binary
                cls
clus              0  1
  SPOP MUTATED    0  4
  SPOP WILD-TYPE  5 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      0    4
  SPOP WILD-TYPE    5   74
     clus
vv    SPOP MUTATED SPOP WILD-TYPE
  NO             0              5
  YES            4             74

Clustering(5) Variable = YBX1 MUTATION ANALYSIS
D5V1, continuous
D5V2, binary
                cls
clus              0  1
  YBX1 MUTATED    0  3
  YBX1 WILD-TYPE  5 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX1 MUTATED      0    3
  YBX1 WILD-TYPE    5   75
     clus
vv    YBX1 MUTATED YBX1 WILD-TYPE
  NO             0              5
  YES            3             75

Clustering(6) Variable = CCNF MUTATION ANALYSIS
D6V1, continuous
D6V2, binary
                cls
clus              0  1
  CCNF MUTATED    1  2
  CCNF WILD-TYPE  4 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNF MUTATED      1    2
  CCNF WILD-TYPE    4   76
     clus
vv    CCNF MUTATED CCNF WILD-TYPE
  NO             1              4
  YES            2             76

Clustering(7) Variable = CLSTN1 MUTATION ANALYSIS
D7V1, continuous
D7V2, binary
                  cls
clus                0  1
  CLSTN1 MUTATED    2  1
  CLSTN1 WILD-TYPE  3 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      2    1
  CLSTN1 WILD-TYPE    3   77
     clus
vv    CLSTN1 MUTATED CLSTN1 WILD-TYPE
  NO               2                3
  YES              1               77

Clustering(8) Variable = PRR21 MUTATION ANALYSIS
D8V1, continuous
D8V2, binary
                 cls
clus               0  1
  PRR21 MUTATED    1  3
  PRR21 WILD-TYPE  4 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRR21 MUTATED      1    3
  PRR21 WILD-TYPE    4   75
     clus
vv    PRR21 MUTATED PRR21 WILD-TYPE
  NO              1               4
  YES             3              75

Clustering(9) Variable = AGT MUTATION ANALYSIS
D9V1, continuous
D9V2, binary
               cls
clus             0  1
  AGT MUTATED    0  3
  AGT WILD-TYPE  5 75
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGT MUTATED      0    3
  AGT WILD-TYPE    5   75
     clus
vv    AGT MUTATED AGT WILD-TYPE
  NO            0             5
  YES           3            75

Clustering(10) Variable = CTNNB1 MUTATION ANALYSIS
D10V1, continuous
D10V2, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    1  2
  CTNNB1 WILD-TYPE  4 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1    2
  CTNNB1 WILD-TYPE    4   76
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               1                4
  YES              2               76

Clustering(11) Variable = DUSP27 MUTATION ANALYSIS
D11V1, continuous
D11V2, binary
                  cls
clus                0  1
  DUSP27 MUTATED    0  3
  DUSP27 WILD-TYPE  5 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP27 MUTATED      0    3
  DUSP27 WILD-TYPE    5   75
     clus
vv    DUSP27 MUTATED DUSP27 WILD-TYPE
  NO               0                5
  YES              3               75

Clustering(12) Variable = OR4D5 MUTATION ANALYSIS
D12V1, continuous
D12V2, binary
                 cls
clus               0  1
  OR4D5 MUTATED    0  3
  OR4D5 WILD-TYPE  5 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D5 MUTATED      0    3
  OR4D5 WILD-TYPE    5   75
     clus
vv    OR4D5 MUTATED OR4D5 WILD-TYPE
  NO              0               5
  YES             3              75

Clustering(13) Variable = OR6N1 MUTATION ANALYSIS
D13V1, continuous
D13V2, binary
                 cls
clus               0  1
  OR6N1 MUTATED    1  2
  OR6N1 WILD-TYPE  4 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6N1 MUTATED      1    2
  OR6N1 WILD-TYPE    4   76
     clus
vv    OR6N1 MUTATED OR6N1 WILD-TYPE
  NO              1               4
  YES             2              76
                                      V1 
                                   "AGE" 
                                      V2 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
> q(save="no")
