
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.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/LIHC/1710369/1.GDAC_mergedClustering.Finished/LIHC.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC/1669677/1.GDAC_clinicalDataPicker.Finished/LIHC.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=62, in cluster file=54, common to both=45
[1]  2 45
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
 9 16 20 
 1  2  3 
 9 16 20 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 8 29  8 
 1  2  3 
 8 29  8 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "NEOADJUVANTTHERAPY"               "BATCHNUMBER"                     

Input Data has 12 rows and 45 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          352           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
          NA         1144          420            2           NA           NA 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-DD-A113 
          NA           NA           NA           NA           NA          217 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
          NA           NA           NA          693           NA           79 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
          NA          652           NA          601           NA          129 
TCGA-EP-A26S TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
         110           37         1175         1231          434          390 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1359           NA          269 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=19,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	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 45 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MIRSEQ_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  2  5
  subtype2  5  8
  subtype3 11  8
subtype1 subtype2 subtype3 
       7       13       19 
subtype1 subtype2 subtype3 
       5        8        8 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A1EL 
       48.99        11.57         1.12         4.24        83.57        13.64 
TCGA-G3-A25S 
        1.22 

$subtype2
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5258 
       37.32        27.52        25.32        69.57         5.03         0.07 
TCGA-DD-A114 TCGA-DD-A119 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       37.74         7.33        38.63        14.27        12.82        44.68 
TCGA-G3-A25Y 
       14.86 

$subtype3
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A216 
       10.13        46.78        27.52         2.99        23.34        37.61 
TCGA-BC-A217 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       13.81         7.13        53.29        22.78         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A25U 
       21.44        51.25        19.76         4.24         3.62        40.47 
TCGA-G3-A25Z 
        8.84 

subtype1 subtype2 subtype3 
    1.12     0.07     0.46 
subtype1 subtype2 subtype3 
   83.57    69.57    53.29 
subtype1 subtype2 subtype3 
   11.57    25.32    19.76 
[1] "1.1 - 83.6 (11.6)" "0.1 - 69.6 (25.3)" "0.5 - 53.3 (19.8)"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype3"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    8    8
  subtype3    8   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        8        8
  MALE          7        8       12

Clustering(2) Variable = MIRSEQ_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1  2  4
  subtype2 12 14
  subtype3  4  3
subtype1 subtype2 subtype3 
       6       26        7 
subtype1 subtype2 subtype3 
       4       14        3 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-DD-A115 TCGA-DD-A1EL TCGA-G3-A25S 
       48.99        11.57         1.12        83.57        13.64         1.22 

$subtype2
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
       69.57         5.03         0.07         7.13        37.74        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EC TCGA-EP-A12J 
       22.78         7.33         0.46        51.25        19.76         4.24 
TCGA-EP-A26S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        3.62        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z 
       14.86         8.84 

$subtype3
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-5263 TCGA-DD-A11A 
       27.52        23.34        37.61        13.81         4.24         2.60 
TCGA-DD-A11C 
       21.44 

subtype1 subtype2 subtype3 
    1.12     0.07     2.60 
subtype1 subtype2 subtype3 
   83.57    69.57    37.61 
subtype1 subtype2 subtype3 
  12.605   17.310   21.440 
[1] "1.1 - 83.6 (12.6)" "0.1 - 69.6 (17.3)" "2.6 - 37.6 (21.4)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    6
  subtype2   14   15
  subtype3    2    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2       14        2
  MALE          6       15        6
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
