
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/jobResults/GDAC_MergedClusteringPipeline/LGG/1552738/1.GDAC_mergedClustering.Finished/LGG.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LGG/1445471/1.GDAC_clinicalDataPicker.Finished/LGG.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=144, in cluster file=67, common to both=67
[1]  4 67
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
 9 10  8 
 1  2  3 
 9 10  8 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
 9  7 11 
 1  2  3 
 9  7 11 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
22 25 20 
 1  2  3 
22 25 20 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
25 15 13 14 
 1  2  3  4 
25 15 13 14 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NEOADJUVANTTHERAPY"                    
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 67 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
         143          234         1335          481          323         1965 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
         857           NA          638          289          194          725 
TCGA-CS-6290 TCGA-CS-6665 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
         546          378         2977         1786         1726         1458 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
        1594         1419         1526         1354          404         1614 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DU-5847 
         607          968          921          438          244          547 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
         442          530           NA          407          257          207 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        5546          576          531          460         6423         1219 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
         682         1491         2286         1401           NA           37 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        2660          213          354           NA          605          511 
TCGA-DU-6407 TCGA-DU-6408 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 
        2875         3469         1525         2051         1251         4084 
TCGA-E1-5318 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        2378         3978          787          407          377          979 
TCGA-FG-6688 
         220 
Variable 1:'AGE':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=62,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 67 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=36, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype2" "subtype1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    6    4
  subtype3    1    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        6        1
  MALE          7        4        7
D1V4, continuous
D1V5, multiclass
D1V6, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2    8    2
  subtype3    4    4
     clus
vv    subtype1 subtype2 subtype3
  NO         7        8        4
  YES        2        2        4
D1V7, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    3    7
  subtype3    3    5
     clus
vv    subtype1 subtype2 subtype3
  NO         5        7        5
  YES        4        3        3

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
 [1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[25] "subtype3" "subtype1"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    1    6
  subtype3    6    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        1        6
  MALE          7        6        5
D2V4, continuous
D2V5, multiclass
D2V6, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2    4    3
  subtype3    8    3
     clus
vv    subtype1 subtype2 subtype3
  NO         7        4        8
  YES        2        3        3
D2V7, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    3    4
  subtype3    3    8
     clus
vv    subtype1 subtype2 subtype3
  NO         5        4        8
  YES        4        3        3

Clustering(3) Variable = MIRSEQ_CNMF
D3V1, survival
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
D3V2, continuous
D3V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    8
  subtype2    9   16
  subtype3   10   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14        9       10
  MALE          8       16       10
D3V4, continuous
D3V5, multiclass
D3V6, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   17
  subtype2    8   17
  subtype3    6   14
     clus
vv    subtype1 subtype2 subtype3
  NO        17       17       14
  YES        5        8        6
D3V7, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    9
  subtype2    7   18
  subtype3    8   12
     clus
vv    subtype1 subtype2 subtype3
  NO         9       18       12
  YES       13        7        8

Clustering(4) Variable = MIRSEQ_CHIERARCHICAL
D4V1, survival
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype4"
[31] "subtype2" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[37] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype4"
[31] "subtype2" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[37] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype4"
[31] "subtype2" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[37] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   17
  subtype2   11    4
  subtype3    9    4
  subtype4    5    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       11        9        5
  MALE         17        4        4        9
D4V4, continuous
D4V5, multiclass
D4V6, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   17
  subtype2    2   13
  subtype3    3   10
  subtype4    6    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       13       10        8
  YES        8        2        3        6
D4V7, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   19
  subtype2    6    9
  subtype3    8    5
  subtype4    8    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        19        9        5        6
  YES        6        6        8        8
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
           "KARNOFSKY.PERFORMANCE.SCORE" 
                                      V5 
                     "HISTOLOGICAL.TYPE" 
                                      V6 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V7 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
