
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.32.3479/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.32.3479/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/133209/BLCA.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA/1445356/1.GDAC_clinicalDataPicker.Finished/BLCA.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=66, in cluster file=28, common to both=28
[1] "Reduce the number of clustering variables from 28 to 1."
[1]  1 28
[1] "NISCH MUTATION ANALYSIS"
[1] 3
  NISCH MUTATED NISCH WILD-TYPE 
              3              25 
  NISCH MUTATED NISCH WILD-TYPE 
              3              25 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "KARNOFSKYPERFORMANCESCORE"       
[11] "NEOADJUVANTTHERAPY"               "BATCHNUMBER"                     

Input Data has 12 rows and 28 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
         389           NA           NA           NA          363           NA 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20V TCGA-BT-A20W TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
          NA           NA           NA           59           88           61 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
          NA           14           13           NA           NA          219 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
          77           NA          273          271 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NISCH MUTATION ANALYSIS
D1V1, survival
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
"NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"NISCH WILD-TYPE" "NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
  "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
"NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"NISCH WILD-TYPE" "NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
  "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
"NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"NISCH WILD-TYPE" "NISCH WILD-TYPE"   "NISCH MUTATED" "NISCH WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
  "NISCH MUTATED" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" "NISCH WILD-TYPE" 
[1] "hr=" "1"  
D1V2, continuous
D1V3, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NISCH MUTATED      2    1
  NISCH WILD-TYPE   16    9
        clus
vv       NISCH MUTATED NISCH WILD-TYPE
  FEMALE             1               9
  MALE               2              16
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
