
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.85.4149/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.85.4149/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/SARC-TP/3537675/SARC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SARC-TP/3353001/SARC-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-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=29, in cluster file=63, common to both=26
[1]  6 26
[1] "CN_CNMF"
[1] 3
1 2 3 
8 5 9 
1 2 3 
8 5 9 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
10 13  3 
 1  2  3 
10 13  3 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 
6 4 
1 2 
6 4 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 
1 3 6 
2 3 
3 6 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 
6 4 
1 2 
6 4 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 
1 3 6 
2 3 
3 6 
[1] "data2feature, selection=ALL"
[1] "YEARSTOBIRTH"                          
[2] "DAYSTODEATH"                           
[3] "DAYSTOLASTFOLLOWUP"                    
[4] "VITALSTATUS"                           
[5] "DCCUPLOADDATE"                         
[6] "GENDER"                                
[7] "RADIATIONTHERAPY"                      
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "BATCHNUMBER"                           

Input Data has 9 rows and 26 columns.

[1] "Batch" "9"    
[1] "Last Follow UP"
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
          62          827           NA          745           NA         1420 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
        1291          960          908         2271           NA           NA 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
         260           NA         1620         1309           14            3 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA 
           2            2          818           NA          126           NA 
TCGA-IW-A3M5 TCGA-KF-A41W 
          NA          181 
Variable 1:'AGE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=17,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'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 26 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=17, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 6 2
  subtype2 2 3
  subtype3 8 1
subtype1 subtype2 subtype3 
       8        5        9 
subtype1 subtype2 subtype3 
       2        3        1 
$subtype1
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-FX-A2QS TCGA-FX-A3RE 
       27.19        12.85        46.68        42.44         0.46         0.07 
TCGA-FX-A48G TCGA-IW-A3M5 
        0.07         5.88 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-HB-A3YV 
        2.04        24.49        18.51         9.70         4.54 

$subtype3
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-HB-A2OT 
       31.56         8.55        53.26        43.04         0.10        26.89 
TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        4.14        13.58         5.95 

subtype1 subtype2 subtype3 
    0.07     2.04     0.10 
subtype1 subtype2 subtype3 
   46.68    24.49    53.26 
subtype1 subtype2 subtype3 
   9.365    9.700   13.580 
[1] "0.1 - 46.7 (9.4)"  "2.0 - 24.5 (9.7)"  "0.1 - 53.3 (13.6)"
 [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype1" "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype1" "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype1" "subtype3"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 5 3
  subtype2 0 5
  subtype3 5 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    3
  subtype2    0    5
  subtype3    5    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        0        5
  MALE          3        5        4

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 8 2
  subtype2 7 6
  subtype3 3 0
subtype1 subtype2 subtype3 
      10       13        3 
subtype1 subtype2 subtype3 
       2        6        0 
$subtype1
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       27.19        24.49        42.44        31.56        29.85         5.23 
TCGA-DX-A23U TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-HB-A2OT 
       76.37        53.26        43.04        26.89 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A2IZ 
        2.04        12.85        18.51        46.68        74.66         8.55 
TCGA-DX-A2J0 TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 
        9.70         0.46         0.07         4.54        13.58         5.88 
TCGA-KF-A41W 
        5.95 

$subtype3
TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A43Z 
        0.10         0.07         4.14 

subtype1 subtype2 subtype3 
    5.23     0.07     0.07 
subtype1 subtype2 subtype3 
   76.37    74.66     4.14 
subtype1 subtype2 subtype3 
  30.705    8.550    0.100 
[1] "5.2 - 76.4 (30.7)" "0.1 - 74.7 (8.6)"  "0.1 - 4.1 (0.1)"  
 [1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[25] "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[25] "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[25] "subtype2" "subtype2"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 4 6
  subtype2 6 7
  subtype3 2 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    6    7
  subtype3    2    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        6        2
  MALE          6        7        1

Clustering(3) Variable = MIRSEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 4 2
  subtype2 3 1
subtype1 subtype2 
       6        4 
subtype1 subtype2 
       2        1 
$subtype1
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-IW-A3M5 
        8.55         9.70        53.26        43.04         0.46         5.88 

$subtype2
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-IS-A3KA 
        0.10         0.07        26.89        13.58 

subtype1 subtype2 
    0.46     0.07 
subtype1 subtype2 
   53.26    26.89 
subtype1 subtype2 
   9.125    6.840 
[1] "0.5 - 53.3 (9.1)" "0.1 - 26.9 (6.8)"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
          cls
clus       0 1
  subtype1 2 4
  subtype2 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    4
  subtype2    3    1
        clus
vv       subtype1 subtype2
  FEMALE        2        3
  MALE          4        1

Clustering(4) Variable = MIRSEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype2 2 1
  subtype3 4 2
subtype2 subtype3 
       3        6 
subtype2 subtype3 
       1        2 
$subtype2
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-IS-A3KA 
        0.10        26.89        13.58 

$subtype3
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-IW-A3M5 
        8.55         9.70        53.26        43.04         0.46         5.88 

subtype2 subtype3 
    0.10     0.46 
subtype2 subtype3 
   26.89    53.26 
subtype2 subtype3 
  13.580    9.125 
[1] "0.1 - 26.9 (13.6)" "0.5 - 53.3 (9.1)" 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
          cls
clus       0 1
  subtype2 2 1
  subtype3 2 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    1
  subtype3    2    4
        clus
vv       subtype2 subtype3
  FEMALE        2        2
  MALE          1        4

Clustering(5) Variable = MIRSEQ_MATURE_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 4 2
  subtype2 3 1
subtype1 subtype2 
       6        4 
subtype1 subtype2 
       2        1 
$subtype1
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-IW-A3M5 
        8.55         9.70        53.26        43.04         0.46         5.88 

$subtype2
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-IS-A3KA 
        0.10         0.07        26.89        13.58 

subtype1 subtype2 
    0.46     0.07 
subtype1 subtype2 
   53.26    26.89 
subtype1 subtype2 
   9.125    6.840 
[1] "0.5 - 53.3 (9.1)" "0.1 - 26.9 (6.8)"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1"
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
          cls
clus       0 1
  subtype1 2 4
  subtype2 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    4
  subtype2    3    1
        clus
vv       subtype1 subtype2
  FEMALE        2        3
  MALE          4        1

Clustering(6) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype2 2 1
  subtype3 4 2
subtype2 subtype3 
       3        6 
subtype2 subtype3 
       1        2 
$subtype2
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-IS-A3KA 
        0.10        26.89        13.58 

$subtype3
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-IW-A3M5 
        8.55         9.70        53.26        43.04         0.46         5.88 

subtype2 subtype3 
    0.10     0.46 
subtype2 subtype3 
   26.89    53.26 
subtype2 subtype3 
  13.580    9.125 
[1] "0.1 - 26.9 (13.6)" "0.5 - 53.3 (9.1)" 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[8] "subtype2" "subtype3"
[1] "hr=" "1.3"
D6V2, continuous
D6V3, binary
          cls
clus       0 1
  subtype2 2 1
  subtype3 2 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    1
  subtype3    2    4
        clus
vv       subtype2 subtype3
  FEMALE        2        2
  MALE          1        4
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
