
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/6225241/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/6154371/ACC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ACC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oT=ACC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/6154371/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/6225241/transformed.cor.cli.txt"

nPatients in clinical file=10, in cluster file=90, common to both=10
[1] "Reduce the number of clustering variables from 10 to 1."
[1]  1 10
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4                6 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4                6 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "GLEASON_SCORE"                         
[14] "PSA_VALUE"                             
[15] "DAYS_TO_PSA"                           
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 10 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO 
          NA           NA         1423          309           NA          889 
TCGA-OR-A5JR TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OU-A5PI 
        3688         1130           NA          709 
Variable 1:'AGE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N"
Output Data has 10 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=10, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=3, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T4 
 3  3  3 
[1] "table(vv)"
vv
T1+T2+T4 
       9 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T4 
 3  3  3 

$nClasses
[1] 1

$ClinVariableType
[1] "multiclass(1)"


T1+T2+T4 
       9 
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CTNNB1 MUTATION ANALYSIS
D1V1, survival
                  sevent
clus2              0 1
  CTNNB1 MUTATED   2 2
  CTNNB1 WILD-TYPE 4 2
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4                6 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               2                2 
$`CTNNB1 MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5K6 TCGA-OR-A5K9 
       10.16        18.05        37.15        11.31 

$`CTNNB1 WILD-TYPE`
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JI TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OU-A5PI 
       18.08        57.53        46.78        29.23       121.25        23.31 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           10.16            18.08 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           37.15           121.25 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          14.680           38.005 
[1] "10.2 - 37.1 (14.7)"  "18.1 - 121.2 (38.0)"
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JI       TCGA-OR-A5JJ 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5JM       TCGA-OR-A5JO       TCGA-OR-A5JR       TCGA-OR-A5K6 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5K9       TCGA-OU-A5PI 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JI       TCGA-OR-A5JJ 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5JM       TCGA-OR-A5JO       TCGA-OR-A5JR       TCGA-OR-A5K6 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5K9       TCGA-OU-A5PI 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" 
      TCGA-OR-A5JB       TCGA-OR-A5JC       TCGA-OR-A5JI       TCGA-OR-A5JJ 
"CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5JM       TCGA-OR-A5JO       TCGA-OR-A5JR       TCGA-OR-A5K6 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" "CTNNB1 WILD-TYPE"   "CTNNB1 MUTATED" 
      TCGA-OR-A5K9       TCGA-OU-A5PI 
  "CTNNB1 MUTATED" "CTNNB1 WILD-TYPE" 
[1] "hr=" "6.8"
D1V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IV
  CTNNB1 MUTATED         0        2        2
  CTNNB1 WILD-TYPE       3        0        2
D1V3, multiclass
          clus
vv         CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I               0                3
  STAGE II              2                0
  STAGE IV              2                2
                  vv
clus               T1+T2+T4
  CTNNB1 MUTATED          4
  CTNNB1 WILD-TYPE        5
[1] "NOT AVAILABLE: table dimension [2x1]"
D1V5, binary
                  cls
clus               0 1
  CTNNB1 MUTATED   3 1
  CTNNB1 WILD-TYPE 2 4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      3    1
  CTNNB1 WILD-TYPE    2    4
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              3                2
  MALE                1                4
> q(save="no")
