
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.84.4098/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.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-WT/3157293/1.GDAC_mergedClustering.Finished/SKCM-WT.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-WT/3215662/SKCM-WT.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=23, in cluster file=35, common to both=23
[1]  8 23
[1] "CN_CNMF"
[1] 3
 1  2 
12 11 
 1  2 
12 11 
[1] "METHLYATION_CNMF"
[1] 3
 1  2 
14  9 
 1  2 
14  9 
[1] "RPPA_CNMF"
[1] 3
 1  2 
10  7 
 1  2 
10  7 
[1] "RPPA_CHIERARCHICAL"
[1] 3
1 2 3 
6 5 6 
1 2 3 
6 5 6 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
 7 14 
 1  2 
 7 14 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 3  6 12 
 1  2  3 
 3  6 12 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2 
13 10 
 1  2 
13 10 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 
8 7 8 
1 2 3 
8 7 8 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 23 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-DA-A3F2 
          NA         2167           NA         1513           NA          870 
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L 
          NA           NA          686         1664         3150           NA 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        2433         2443           NA           NA           NA           NA 
TCGA-FS-A1ZU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T1 T1A  T2 T2A T3A T3B  T4 T4A T4B  TX 
  2   1   2   1   3   2   1   2   5   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 23 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=6, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 9
  subtype2 6 5
subtype1 subtype2 
      12       11 
subtype1 subtype2 
       9        5 
$subtype1
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A3ET 
       43.40        71.24        65.92         8.65        13.97        80.32 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A264 TCGA-GN-A26D 
        9.70        47.38        23.93        26.56       117.93        39.58 

$subtype2
TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A3F2 TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR 
       24.53        49.74        28.60        22.55        54.71       103.56 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FS-A1Z4 TCGA-GN-A261 TCGA-GN-A26A 
      131.08        79.99        28.08        76.41        32.48 

subtype1 subtype2 
    8.65    22.55 
subtype1 subtype2 
  117.93   131.08 
subtype1 subtype2 
   41.49    49.74 
[1] "8.7 - 117.9 (41.5)"  "22.6 - 131.1 (49.7)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[1] "hr=" "2.6"
D1V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        4
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   7
  subtype2                   7
D1V3, multiclass
D1V4, binary
          cls
clus       0 1
  subtype1 7 5
  subtype2 5 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2    5    6
        clus
vv       subtype1 subtype2
  FEMALE        7        5
  MALE          5        6
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  7  0   1   2   1  0
  subtype2  4  1   1   1   1  2
D1V5, multiclass
D1V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0        1         2         3         0          1
  subtype2       3        1        0         0         0         1          1
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          1          2
  subtype2          1          2
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  4 10
  subtype2  5  4
subtype1 subtype2 
      14        9 
subtype1 subtype2 
      10        4 
$subtype1
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D9-A149 TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D 
       43.40        71.24        49.74        65.92         8.65        13.97 
TCGA-ER-A19L TCGA-ER-A3ET TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU 
      131.08        80.32         9.70        47.38        23.93        26.56 
TCGA-GN-A264 TCGA-GN-A26D 
      117.93        39.58 

$subtype2
TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A1A1 
       24.53        28.60        22.55        54.71       103.56        79.99 
TCGA-FS-A1Z4 TCGA-GN-A261 TCGA-GN-A26A 
       28.08        76.41        32.48 

subtype1 subtype2 
    8.65    22.55 
subtype1 subtype2 
  131.08   103.56 
subtype1 subtype2 
   45.39    32.48 
[1] "8.7 - 131.1 (45.4)"  "22.6 - 103.6 (32.5)"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[1] "hr=" "1.4"
D2V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        3
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   8
  subtype2                   6
D2V3, multiclass
D2V4, binary
          cls
clus       0 1
  subtype1 8 6
  subtype2 4 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2    4    5
        clus
vv       subtype1 subtype2
  FEMALE        8        4
  MALE          6        5
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  7  0   1   3   1  0
  subtype2  4  1   1   0   1  2
D2V5, multiclass
D2V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0        1         2         3         0          1
  subtype2       3        1        0         0         0         1          1
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          1          2
  subtype2          1          2
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 7
  subtype2 3 4
subtype1 subtype2 
      10        7 
subtype1 subtype2 
       7        4 
$subtype1
TCGA-D3-A2J6 TCGA-D9-A149 TCGA-DA-A1IA TCGA-ER-A1A1 TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       43.40        49.74        65.92        79.99         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A264 TCGA-GN-A26D 
       23.93        26.56       117.93        39.58 

$subtype2
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L TCGA-FS-A1Z4 TCGA-GN-A261 
       22.55        54.71       103.56       131.08        28.08        76.41 
TCGA-GN-A26A 
       32.48 

subtype1 subtype2 
    9.70    22.55 
subtype1 subtype2 
  117.93   131.08 
subtype1 subtype2 
   45.39    54.71 
[1] "9.7 - 117.9 (45.4)"  "22.6 - 131.1 (54.7)"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[1] "hr=" "2"  
D3V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   6
  subtype2                   5
D3V3, multiclass
D3V4, binary
          cls
clus       0 1
  subtype1 6 4
  subtype2 3 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    4
  subtype2    3    4
        clus
vv       subtype1 subtype2
  FEMALE        6        3
  MALE          4        4
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  5  0   0   2   1  1
  subtype2  4  1   1   0   0  0
D3V5, multiclass
D3V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0        1         1         2         0          0
  subtype2       3        1        0         0         0         1          1
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          1          2
  subtype2          0          0
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 3 3
  subtype2 1 4
  subtype3 2 4
subtype1 subtype2 subtype3 
       6        5        6 
subtype1 subtype2 subtype3 
       3        4        4 
$subtype1
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-FS-A1Z4 TCGA-GN-A261 TCGA-GN-A26A 
       22.55        54.71       103.56        28.08        76.41        32.48 

$subtype2
TCGA-ER-A19L TCGA-FS-A1ZJ TCGA-FS-A1ZU TCGA-GN-A264 TCGA-GN-A26D 
      131.08        47.38        26.56       117.93        39.58 

$subtype3
TCGA-D3-A2J6 TCGA-D9-A149 TCGA-DA-A1IA TCGA-ER-A1A1 TCGA-FS-A1ZG TCGA-FS-A1ZK 
       43.40        49.74        65.92        79.99         9.70        23.93 

subtype1 subtype2 subtype3 
   22.55    26.56     9.70 
subtype1 subtype2 subtype3 
  103.56   131.08    79.99 
subtype1 subtype2 subtype3 
  43.595   47.380   46.570 
[1] "22.6 - 103.6 (43.6)" "26.6 - 131.1 (47.4)" "9.7 - 80.0 (46.6)"  
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
D4V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  1
  subtype3                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        0
  subtype3                                                                                        1
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   4
  subtype2                   4
  subtype3                   3
D4V3, multiclass
D4V4, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 3 2
  subtype3 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    3    2
  subtype3    3    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        3        3
  MALE          3        2        3
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  4  1   1   0   0  0
  subtype2  3  0   0   0   0  0
  subtype3  2  0   0   2   1  1
D4V5, multiclass
D4V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       3        1        0         0         0         1          1
  subtype2       1        0        0         0         2         0          0
  subtype3       0        0        1         1         0         0          0
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          0          0
  subtype2          0          0
  subtype3          1          2
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  5  2
  subtype2  2 12
subtype1 subtype2 
       7       14 
subtype1 subtype2 
       2       12 
$subtype1
TCGA-D3-A3CF TCGA-D9-A149 TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A1A1 
       24.53        49.74        22.55        54.71       103.56        79.99 
TCGA-FS-A1Z4 
       28.08 

$subtype2
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       43.40        71.24        65.92         8.65        13.97       131.08 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A261 TCGA-GN-A264 
        9.70        47.38        23.93        26.56        76.41       117.93 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

subtype1 subtype2 
   22.55     8.65 
subtype1 subtype2 
  103.56   131.08 
subtype1 subtype2 
   49.74    41.49 
[1] "22.6 - 103.6 (49.7)" "8.7 - 131.1 (41.5)" 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
[1] "hr=" "2.7"
D5V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   6
  subtype2                   8
D5V3, multiclass
D5V4, binary
          cls
clus       0 1
  subtype1 3 4
  subtype2 8 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    4
  subtype2    8    6
        clus
vv       subtype1 subtype2
  FEMALE        3        8
  MALE          4        6
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  4  0   0   1   0  2
  subtype2  7  1   1   2   1  0
D5V5, multiclass
D5V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       3        1        0         0         0         0          0
  subtype2       1        0        1         2         3         1          1
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          0          2
  subtype2          1          2
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  2  1
  subtype2  4  2
  subtype3  1 11
subtype1 subtype2 subtype3 
       3        6       12 
subtype1 subtype2 subtype3 
       1        2       11 
$subtype1
TCGA-EE-A2GI TCGA-GN-A26A TCGA-GN-A26D 
       22.55        32.48        39.58 

$subtype2
TCGA-D3-A3CF TCGA-D9-A149 TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A1A1 TCGA-FS-A1Z4 
       24.53        49.74        54.71       103.56        79.99        28.08 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       43.40        71.24        65.92         8.65        13.97       131.08 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A261 TCGA-GN-A264 
        9.70        47.38        23.93        26.56        76.41       117.93 

subtype1 subtype2 subtype3 
   22.55    24.53     8.65 
subtype1 subtype2 subtype3 
   39.58   103.56   131.08 
subtype1 subtype2 subtype3 
  32.480   52.225   45.390 
[1] "22.6 - 39.6 (32.5)"  "24.5 - 103.6 (52.2)" "8.7 - 131.1 (45.4)" 
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1"
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1"
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1"
D6V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  0
  subtype3                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
  subtype3                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   2
  subtype2                   5
  subtype3                   7
D6V3, multiclass
D6V4, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 3 3
  subtype3 6 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    3    3
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        3        6
  MALE          1        3        6
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  2  0   1   0   0  0
  subtype2  3  0   0   1   0  2
  subtype3  6  1   0   2   1  0
D6V5, multiclass
D6V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       0        1        0         0         1         0          1
  subtype2       3        0        0         0         0         0          0
  subtype3       1        0        1         2         2         1          0
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          0          0
  subtype2          0          2
  subtype3          1          2
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  3 10
  subtype2  6  4
subtype1 subtype2 
      13       10 
subtype1 subtype2 
      10        4 
$subtype1
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D 
       43.40        24.53        49.74        65.92         8.65        13.97 
TCGA-EE-A2GI TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-GN-A264 
       22.55         9.70        47.38        23.93        26.56       117.93 
TCGA-GN-A26D 
       39.58 

$subtype2
TCGA-D3-A3CC TCGA-DA-A3F2 TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L TCGA-ER-A1A1 
       71.24        28.60        54.71       103.56       131.08        79.99 
TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-GN-A261 TCGA-GN-A26A 
       80.32        28.08        76.41        32.48 

subtype1 subtype2 
    8.65    28.08 
subtype1 subtype2 
  117.93   131.08 
subtype1 subtype2 
  26.560   73.825 
[1] "8.7 - 117.9 (26.6)"  "28.1 - 131.1 (73.8)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[1] "hr=" "5"  
D7V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        5
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   9
  subtype2                   5
D7V3, multiclass
D7V4, binary
          cls
clus       0 1
  subtype1 7 6
  subtype2 5 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    6
  subtype2    5    5
        clus
vv       subtype1 subtype2
  FEMALE        7        5
  MALE          6        5
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  7  0   0   3   1  1
  subtype2  4  1   2   0   1  1
D7V5, multiclass
D7V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        1        1         2         2         0          0
  subtype2       3        0        0         0         1         1          2
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          1          3
  subtype2          1          1
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 4 4
  subtype2 2 5
  subtype3 3 5
subtype1 subtype2 subtype3 
       8        7        8 
subtype1 subtype2 subtype3 
       4        5        5 
$subtype1
TCGA-DA-A3F2 TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FS-A1Z4 
       28.60        54.71       103.56       131.08        79.99        28.08 
TCGA-GN-A261 TCGA-GN-A26A 
       76.41        32.48 

$subtype2
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2GI TCGA-ER-A3ET TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        8.65        13.97        22.55        80.32         9.70        47.38 
TCGA-GN-A264 
      117.93 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-FS-A1ZK 
       43.40        71.24        24.53        49.74        65.92        23.93 
TCGA-FS-A1ZU TCGA-GN-A26D 
       26.56        39.58 

subtype1 subtype2 subtype3 
   28.08     8.65    23.93 
subtype1 subtype2 subtype3 
  131.08   117.93    71.24 
subtype1 subtype2 subtype3 
   65.56    22.55    41.49 
[1] "28.1 - 131.1 (65.6)" "8.7 - 117.9 (22.6)"  "23.9 - 71.2 (41.5)" 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
D8V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  0
  subtype3                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        3
  subtype2                                                                                        1
  subtype3                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   5
  subtype2                   6
  subtype3                   3
D8V3, multiclass
D8V4, binary
          cls
clus       0 1
  subtype1 3 5
  subtype2 3 4
  subtype3 6 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    5
  subtype2    3    4
  subtype3    6    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        3        6
  MALE          5        4        2
          vv
clus       N0 N1 N1A N1B N2B N3
  subtype1  3  1   1   0   1  1
  subtype2  3  0   1   1   1  0
  subtype3  5  0   0   2   0  1
D8V5, multiclass
D8V6, continuous
          vv
clus       STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       3        0        0         0         0         1          1
  subtype2       1        1        0         1         0         0          1
  subtype3       0        0        1         1         3         0          0
          vv
clus       STAGE IIIB STAGE IIIC
  subtype1          1          1
  subtype2          0          2
  subtype3          1          1
D8V7, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"   "LYMPH.NODE.METASTASIS"         "TUMOR.STAGECODE" 
                       V7 
  "NEOPLASM.DISEASESTAGE" 
> q(save="no")
