
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.59.3844/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.59.3844/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/CESC/1710370/1.GDAC_mergedClustering.Finished/CESC.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC/1669572/1.GDAC_clinicalDataPicker.Finished/CESC.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-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=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=32, in cluster file=42, common to both=17
[1]  2 17
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 
9 4 4 
1 2 3 
9 4 4 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 
3 1 3 2 8 
1 3 5 
3 3 8 
[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] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 17 columns.

[1] "Batch" "12"   
[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-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
        2127         2892           NA           NA           NA          376 
TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        3096            8          178           37           37 
Variable 1:'AGE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
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=9,	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=FALSE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 17 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=13, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MIRSEQ_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 7 2
  subtype2 3 1
  subtype3 3 1
subtype1 subtype2 subtype3 
       9        4        4 
subtype1 subtype2 subtype3 
       2        1        1 
$subtype1
TCGA-BI-A0VR TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1OA TCGA-DS-A1OD 
       49.48        42.38        36.76         2.66        28.90       101.79 
TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23L 
        0.26         5.85         1.22 

$subtype2
TCGA-BI-A0VS TCGA-DS-A1OB TCGA-DS-A1OC TCGA-FU-A23K 
       30.41        28.27        12.36         1.22 

$subtype3
TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
       70.85        69.93        95.08         8.75 

subtype1 subtype2 subtype3 
    0.26     1.22     8.75 
subtype1 subtype2 subtype3 
  101.79    30.41    95.08 
subtype1 subtype2 subtype3 
  28.900   20.315   70.390 
[1] "0.3 - 101.8 (28.9)" "1.2 - 30.4 (20.3)"  "8.8 - 95.1 (70.4)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    2    2
  subtype3    1    3
     clus
vv    subtype1 subtype2 subtype3
  NO         3        2        1
  YES        6        2        3
D1V4, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    2    2
  subtype3    2    2
     clus
vv    subtype1 subtype2 subtype3
  NO         2        2        2
  YES        7        2        2

Clustering(2) Variable = MIRSEQ_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype3 2 1
  subtype5 6 2
subtype1 subtype3 subtype5 
       3        3        8 
subtype1 subtype3 subtype5 
       0        1        2 
$subtype1
TCGA-BI-A0VS TCGA-DS-A1OC TCGA-FU-A23L 
       30.41        12.36         1.22 

$subtype3
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
       69.93        95.08         8.75 

$subtype5
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1OA 
       49.48        70.85        42.38        36.76         2.66        28.90 
TCGA-EA-A1QT TCGA-EX-A1H5 
        0.26         5.85 

subtype1 subtype3 subtype5 
    1.22     8.75     0.26 
subtype1 subtype3 subtype5 
   30.41    95.08    70.85 
subtype1 subtype3 subtype5 
   12.36    69.93    32.83 
[1] "1.2 - 30.4 (12.4)" "8.8 - 95.1 (69.9)" "0.3 - 70.8 (32.8)"
 [1] "subtype5" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
 [7] "subtype3" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[13] "subtype5" "subtype1"
 [1] "subtype5" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
 [7] "subtype3" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[13] "subtype5" "subtype1"
 [1] "subtype5" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
 [7] "subtype3" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[13] "subtype5" "subtype1"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype3    1    2
  subtype5    2    6
     clus
vv    subtype1 subtype3 subtype5
  NO         1        1        2
  YES        2        2        6
D2V4, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype3    2    1
  subtype5    1    7
     clus
vv    subtype1 subtype3 subtype5
  NO         1        2        1
  YES        2        1        7
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
