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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.36.3689/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.36.3689/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/302130/CESC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2330179/1.GDAC_clinicalDataPicker.Finished/CESC-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=32, in cluster file=36, common to both=12
[1] "Reduce the number of clustering variables from 2 to 1."
[1]  1 12
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3                9 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3                9 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 12 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1505          925         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        2127         2892            8          178           37           37 
Variable 1:'AGE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'STOPPEDSMOKINGYEAR':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                            "NUMBERPACKYEARSSMOKED"         
[3] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 12 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=10, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=3, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=3, binary=FALSE, numeric=TRUE

Clustering(1) Variable = NFE2L2 MUTATION ANALYSIS
D1V1, survival
                  sevent
clus2              0 1
  NFE2L2 MUTATED   2 1
  NFE2L2 WILD-TYPE 9 0
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3                9 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1                0 
$`NFE2L2 MUTATED`
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       42.38        65.62        65.85 

$`NFE2L2 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT 
       49.48        30.41        65.88         2.66        65.85         0.26 
TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        5.85         1.22         1.22 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           42.38             0.26 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           65.85            65.88 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           65.62             5.85 
[1] "42.4 - 65.8 (65.6)" "0.3 - 65.9 (5.8)"  
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K       TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K       TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" 
      TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K       TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
[1] "hr="     "1.6e+09"
D1V2, continuous
D1V3, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"         "NFE2L2 WILD-TYPE"      
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1                2 
named character(0)
D1V4, continuous
                            V1.D                               V2 
                 "Time to Death"                            "AGE" 
                              V3                               V4 
         "NUMBERPACKYEARSSMOKED" "TOBACCOSMOKINGHISTORYINDICATOR" 
> q(save="no")
