
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/BLCA/1590604/1.GDAC_mergedClustering.Finished/BLCA.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA/1551038/1.GDAC_clinicalDataPicker.Finished/BLCA.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=67, in cluster file=88, common to both=66
[1]  5 66
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
18 26 21 
 1  2  3 
18 26 21 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
18 14 
 1  2 
18 14 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
12  8 12 
 1  2  3 
12  8 12 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
12 29 10  3 12 
 1  2  3  4  5 
12 29 10  3 12 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 2 12 52 
 2  3 
12 52 
[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 66 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
         389           NA           NA           NA           NA          363 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-C4-A0EZ 
          NA           NA           NA           NA           NA           NA 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
          59           88           61           NA           14           13 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 
          21           NA           NA          219           77           NA 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
         955          273          214          271         3616         3056 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
         218          178          202           55          322           NA 
TCGA-DK-A2I6 TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        2291         1108          268          253           NA          209 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
          NA          336           71          417         1497          806 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
         172           NA          684          525          214           NA 
TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
          68          234          160          187           46          204 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=40,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE

Clustering(1) Variable = METHLYATION_CNMF
D1V1, survival
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    8
  subtype2   15   11
  subtype3   17    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       11        4
  MALE         10       15       17
D1V4, continuous

Clustering(2) Variable = MRNASEQ_CNMF
D2V1, survival
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1"
[1] "hr=" "2.6"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    4
  subtype2    8    6
        clus
vv       subtype1 subtype2
  FEMALE        4        6
  MALE         14        8
D2V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)

Clustering(3) Variable = MRNASEQ_CHIERARCHICAL
D3V1, survival
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype2"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype2"
D3V2, continuous
D3V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    6
  subtype2    7    1
  subtype3    9    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6        1        3
  MALE          6        7        9
D3V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       1 
character(0)

Clustering(4) Variable = MIRSEQ_CNMF
D4V1, survival
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype5" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype5" "subtype2" "subtype3" "subtype2" "subtype2"
[55] "subtype5" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype5" "subtype3" "subtype4" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype5" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype5" "subtype2" "subtype3" "subtype2" "subtype2"
[55] "subtype5" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype5" "subtype3" "subtype4" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype5" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype5" "subtype2" "subtype3" "subtype2" "subtype2"
[55] "subtype5" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype5" "subtype3" "subtype4" "subtype1" "subtype1"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    3
  subtype2   19   10
  subtype3    6    4
  subtype4    2    1
  subtype5    7    5
D4V4, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       8        5        1        2 
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype3"

Clustering(5) Variable = MIRSEQ_CHIERARCHICAL
D5V1, survival
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype2"
[1] "hr=" "1.5"
D5V2, continuous
D5V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    8    4
  subtype3   33   19
        clus
vv       subtype2 subtype3
  FEMALE        4       19
  MALE          8       33
D5V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       1       14 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3"
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
> q(save="no")
