
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-NRAS_Hotspot_Mutants/3157510/1.GDAC_mergedClustering.Finished/SKCM-NRAS_Hotspot_Mutants.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NRAS_Hotspot_Mutants/3215657/SKCM-NRAS_Hotspot_Mutants.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=45, in cluster file=62, common to both=45
[1]  8 45
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
12  8 12 13 
 1  2  3  4 
12  8 12 13 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
15 14 16 
 1  2  3 
15 14 16 
[1] "RPPA_CNMF"
[1] 3
 1  2 
16 14 
 1  2 
16 14 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
 3  4  1  5  7 10 
 1  2  4  5  6 
 3  4  5  7 10 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
18 15 12 
 1  2  3 
18 15 12 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 9 16 20 
 1  2  3 
 9 16 20 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
 9  6 15 15 
 1  2  3  4 
 9  6 15 15 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 5  9 31 
 1  2  3 
 5  9 31 
[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 45 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
          NA           NA           NA          164         1484         1192 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
          NA           NA           NA           NA          247          269 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
         304           NA           NA          769          727           NA 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AC TCGA-ER-A19D TCGA-ER-A19N TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
          NA           NA         1303           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZY TCGA-GN-A267 TCGA-GN-A268 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=21,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	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
 T0 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B  TX 
  4   4   2   4   5   3   1   5   4   1   2   6   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 45 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=28, 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=13, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 6
  subtype2 0 3
  subtype3 4 1
  subtype4 2 3
subtype1 subtype2 subtype3 subtype4 
       9        3        5        5 
subtype1 subtype2 subtype3 subtype4 
       6        3        1        3 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A185 TCGA-EE-A29S TCGA-EE-A29V 
       16.47         5.39        48.79         4.27         9.99         2.43 
TCGA-EE-A29X TCGA-GN-A267 TCGA-GN-A268 
        8.09        16.21        15.39 

$subtype2
TCGA-D3-A1Q8 TCGA-EE-A17X TCGA-ER-A19D 
       28.08        11.57         3.52 

$subtype3
TCGA-D3-A2J8 TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19N 
        8.38         8.12        25.28        23.90        42.84 

$subtype4
TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A5 
       39.19         7.00         1.08         8.84         9.67 

subtype1 subtype2 subtype3 subtype4 
    2.43     3.52     8.12     1.08 
subtype1 subtype2 subtype3 subtype4 
   48.79    28.08    42.84    39.19 
subtype1 subtype2 subtype3 subtype4 
    9.99    11.57    23.90     8.84 
[1] "2.4 - 48.8 (10.0)" "3.5 - 28.1 (11.6)" "8.1 - 42.8 (23.9)"
[4] "1.1 - 39.2 (8.8)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype4"
 [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype3" "subtype4"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype4"
[19] "subtype2" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype4"
 [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype3" "subtype4"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype4"
[19] "subtype2" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype4"
 [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype3" "subtype4"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype4"
[19] "subtype2" "subtype3" "subtype1" "subtype1"
D1V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  1
  subtype3                  1
  subtype4                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        2
  subtype3                                                                                        2
  subtype4                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   7
  subtype2                   5
  subtype3                   9
  subtype4                   7
D1V3, multiclass
D1V4, binary
          cls
clus        0  1
  subtype1  6  6
  subtype2  4  4
  subtype3  3  9
  subtype4  3 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    6
  subtype2    4    4
  subtype3    3    9
  subtype4    3   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        4        3        3
  MALE          6        4        9       10
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1  5   2   1   1   1  2
  subtype2  6   0   0   0   0  1
  subtype3  8   1   1   0   0  0
  subtype4  8   0   2   0   1  2
D1V5, multiclass
D1V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       0        0        1        0         1         1
  subtype2           0       1        1        1        2         0         0
  subtype3           0       1        0        3        1         1         2
  subtype4           0       1        3        1        1         1         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          1          3          3        0
  subtype2         1         0          0          0          0        1
  subtype3         0         0          0          2          0        0
  subtype4         0         1          0          1          3        0
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 1 5
  subtype2 3 3
  subtype3 5 5
subtype1 subtype2 subtype3 
       6        6       10 
subtype1 subtype2 subtype3 
       5        3        5 
$subtype1
TCGA-D3-A1Q1 TCGA-DA-A3F3 TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
       16.47         7.00         8.84         9.67         3.52        16.21 

$subtype2
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-EE-A29V TCGA-EE-A2A1 TCGA-ER-A19N 
       28.08         8.38         5.39         2.43        25.28        42.84 

$subtype3
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q 
       48.79        39.19        11.57         4.27         1.08         8.12 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-GN-A268 
        9.99         8.09        23.90        15.39 

subtype1 subtype2 subtype3 
    3.52     2.43     1.08 
subtype1 subtype2 subtype3 
   16.47    42.84    48.79 
subtype1 subtype2 subtype3 
   9.255   16.830   10.780 
[1] "3.5 - 16.5 (9.3)"  "2.4 - 42.8 (16.8)" "1.1 - 48.8 (10.8)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
D2V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  4
  subtype2                  4
  subtype3                  0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        4
  subtype2                                                                                        2
  subtype3                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   7
  subtype2                   8
  subtype3                  13
D2V3, multiclass
D2V4, binary
          cls
clus        0  1
  subtype1  5 10
  subtype2  3 11
  subtype3  8  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   10
  subtype2    3   11
  subtype3    8    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        3        8
  MALE         10       11        8
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1  8   2   1   0   1  1
  subtype2  8   1   2   1   0  1
  subtype3 11   0   1   0   1  3
D2V5, multiclass
D2V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       0        1        3        1         1         1
  subtype2           1       1        0        2        2         1         1
  subtype3           0       2        3        1        1         1         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          1          2          2        0
  subtype2         0         1          0          2          1        1
  subtype3         1         0          0          2          3        0
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 4
  subtype2 2 6
subtype1 subtype2 
       7        8 
subtype1 subtype2 
       4        6 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N 
       16.47        28.08        48.79        23.90         3.52        42.84 
TCGA-GN-A267 
       16.21 

$subtype2
TCGA-D3-A2J8 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
        8.38        11.57         4.27         1.08         8.84         9.99 
TCGA-EE-A29V TCGA-GN-A268 
        2.43        15.39 

subtype1 subtype2 
    3.52     1.08 
subtype1 subtype2 
   48.79    15.39 
subtype1 subtype2 
   23.90     8.61 
[1] "3.5 - 48.8 (23.9)" "1.1 - 15.4 (8.6)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2"
[1] "hr=" "11" 
D3V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  13
  subtype2                  10
D3V3, multiclass
D3V4, binary
          cls
clus        0  1
  subtype1  7  9
  subtype2  4 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2    4   10
        clus
vv       subtype1 subtype2
  FEMALE        7        4
  MALE          9       10
          vv
clus       N0 N1A N1B N2B N3
  subtype1  8   1   2   1  2
  subtype2  8   1   2   0  2
D3V5, multiclass
D3V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       2        2        2        1         1         0
  subtype2           1       1        1        1        2         1         1
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1          1          2          1        1
  subtype2         0          0          1          4        0
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 1 0
  subtype2 0 2
  subtype4 1 4
  subtype5 3 0
  subtype6 0 4
subtype1 subtype2 subtype4 subtype5 subtype6 
       1        2        5        3        4 
subtype1 subtype2 subtype4 subtype5 subtype6 
       0        2        4        0        4 
$subtype1
TCGA-EE-A29S 
        9.99 

$subtype2
TCGA-D3-A2J8 TCGA-EE-A29V 
        8.38         2.43 

$subtype4
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-EE-A29R TCGA-ER-A19D TCGA-GN-A267 
       16.47        28.08         8.84         3.52        16.21 

$subtype5
TCGA-DA-A1HV TCGA-EE-A2A2 TCGA-ER-A19N 
       48.79        23.90        42.84 

$subtype6
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-GN-A268 
       11.57         4.27         1.08        15.39 

subtype1 subtype2 subtype4 subtype5 subtype6 
    9.99     2.43     3.52    23.90     1.08 
subtype1 subtype2 subtype4 subtype5 subtype6 
    9.99     8.38    28.08    48.79    15.39 
subtype1 subtype2 subtype4 subtype5 subtype6 
   9.990    5.405   16.210   42.840    7.920 
[1] "10.0 - 10.0 (10.0)" "2.4 - 8.4 (5.4)"    "3.5 - 28.1 (16.2)" 
[4] "23.9 - 48.8 (42.8)" "1.1 - 15.4 (7.9)"  
 [1] "subtype4" "subtype4" "subtype2" "subtype5" "subtype6" "subtype6"
 [7] "subtype6" "subtype4" "subtype1" "subtype2" "subtype5" "subtype4"
[13] "subtype5" "subtype4" "subtype6"
 [1] "subtype4" "subtype4" "subtype2" "subtype5" "subtype6" "subtype6"
 [7] "subtype6" "subtype4" "subtype1" "subtype2" "subtype5" "subtype4"
[13] "subtype5" "subtype4" "subtype6"
 [1] "subtype4" "subtype4" "subtype2" "subtype5" "subtype6" "subtype6"
 [7] "subtype6" "subtype4" "subtype1" "subtype2" "subtype5" "subtype4"
[13] "subtype5" "subtype4" "subtype6"
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype4 subtype5 subtype6 
       1        2        5        3        4 
 [1] "subtype4" "subtype4" "subtype5" "subtype6" "subtype6" "subtype6"
 [7] "subtype4" "subtype5" "subtype4" "subtype5" "subtype4" "subtype6"
D4V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  1
  subtype4                  0
  subtype5                  0
  subtype6                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        0
  subtype2                                                                                        1
  subtype4                                                                                        1
  subtype5                                                                                        0
  subtype6                                                                                        0
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   3
  subtype2                   2
  subtype4                   4
  subtype5                   7
  subtype6                   7
D4V3, multiclass
D4V4, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 0 4
  subtype4 3 2
  subtype5 3 4
  subtype6 3 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    0    4
  subtype4    3    2
  subtype5    3    4
  subtype6    3    7
          vv
clus       N0 N1A N1B N2B N3
  subtype1  3   0   0   0  0
  subtype2  2   1   1   0  0
  subtype4  1   1   1   0  2
  subtype5  3   0   1   1  0
  subtype6  6   0   1   0  2
D4V5, multiclass
D4V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       0        0        0        1         2         0
  subtype2           0       1        0        1        0         0         0
  subtype4           0       0        0        1        0         0         0
  subtype5           0       2        1        0        0         0         0
  subtype6           1       0        1        1        2         0         1
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0          0          0          0        0
  subtype2         0          0          1          1        0
  subtype4         0          1          0          2        1
  subtype5         0          0          2          0        0
  subtype6         1          0          0          2        0
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 2 6
  subtype2 6 1
  subtype3 1 6
subtype1 subtype2 subtype3 
       8        7        7 
subtype1 subtype2 subtype3 
       6        1        6 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A29R TCGA-EE-A2A5 
       16.47        28.08         5.39         7.00         8.84         9.67 
TCGA-ER-A19D TCGA-GN-A267 
        3.52        16.21 

$subtype2
TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.38        48.79        39.19         9.99        25.28        23.90 
TCGA-ER-A19N 
       42.84 

$subtype3
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         1.08         8.12         2.43         8.09 
TCGA-GN-A268 
       15.39 

subtype1 subtype2 subtype3 
    3.52     8.38     1.08 
subtype1 subtype2 subtype3 
   28.08    48.79    15.39 
subtype1 subtype2 subtype3 
   9.255   25.280    8.090 
[1] "3.5 - 28.1 (9.3)"  "8.4 - 48.8 (25.3)" "1.1 - 15.4 (8.1)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3"
D5V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  3
  subtype2                  1
  subtype3                  4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        7
  subtype2                                                                                        1
  subtype3                                                                                        1
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   8
  subtype2                  13
  subtype3                   7
D5V3, multiclass
D5V4, binary
          cls
clus        0  1
  subtype1  9  9
  subtype2  2 13
  subtype3  5  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    9
  subtype2    2   13
  subtype3    5    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        2        5
  MALE          9       13        7
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1 10   2   1   1   1  2
  subtype2  8   1   2   0   1  1
  subtype3  9   0   1   0   0  2
D5V5, multiclass
D5V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       1        1        3        1         1         2
  subtype2           0       2        1        2        1         2         0
  subtype3           1       0        2        1        2         0         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          1          3          2        1
  subtype2         0         1          0          3          1        0
  subtype3         1         0          0          0          3        0
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 0 6
  subtype2 5 2
  subtype3 4 5
subtype1 subtype2 subtype3 
       6        7        9 
subtype1 subtype2 subtype3 
       6        2        5 
$subtype1
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29X TCGA-GN-A268 
       11.57         4.27         1.08         2.43         8.09        15.39 

$subtype2
TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29S TCGA-EE-A2A2 TCGA-ER-A19N 
        8.38        48.79        39.19         9.99        23.90        42.84 
TCGA-GN-A267 
       16.21 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A29Q TCGA-EE-A29R 
       16.47        28.08         5.39         7.00         8.12         8.84 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
       25.28         9.67         3.52 

subtype1 subtype2 subtype3 
    1.08     8.38     3.52 
subtype1 subtype2 subtype3 
   15.39    48.79    28.08 
subtype1 subtype2 subtype3 
    6.18    23.90     8.84 
[1] "1.1 - 15.4 (6.2)"  "8.4 - 48.8 (23.9)" "3.5 - 28.1 (8.8)" 
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1"
D6V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  4
  subtype2                  0
  subtype3                  4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        0
  subtype2                                                                                        1
  subtype3                                                                                        8
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   5
  subtype2                  15
  subtype3                   8
D6V3, multiclass
D6V4, binary
          cls
clus        0  1
  subtype1  3  6
  subtype2  3 13
  subtype3 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    3   13
  subtype3   10   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        3       10
  MALE          6       13       10
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1  6   0   1   0   0  2
  subtype2  9   2   1   0   1  1
  subtype3 12   1   2   1   1  2
D6V5, multiclass
D6V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       0        1        1        1         0         1
  subtype2           0       2        2        1        2         2         0
  subtype3           0       1        1        4        1         1         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          0          0          3        0
  subtype2         0         0          1          3          1        0
  subtype3         1         1          0          3          2        1
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 0 3
  subtype2 2 1
  subtype3 5 4
  subtype4 2 5
subtype1 subtype2 subtype3 subtype4 
       3        3        9        7 
subtype1 subtype2 subtype3 subtype4 
       3        1        4        5 
$subtype1
TCGA-D3-A1Q1 TCGA-EE-A17X TCGA-EE-A29X 
       16.47        11.57         8.09 

$subtype2
TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-EE-A2A2 
       28.08         5.39        23.90 

$subtype3
TCGA-D3-A2J8 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
        8.38         8.12         8.84         9.99         2.43        25.28 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        9.67         3.52        42.84 

$subtype4
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L TCGA-GN-A267 
       48.79        39.19         7.00         4.27         1.08        16.21 
TCGA-GN-A268 
       15.39 

subtype1 subtype2 subtype3 subtype4 
    8.09     5.39     2.43     1.08 
subtype1 subtype2 subtype3 subtype4 
   16.47    28.08    42.84    48.79 
subtype1 subtype2 subtype3 subtype4 
   11.57    23.90     8.84    15.39 
[1] "8.1 - 16.5 (11.6)" "5.4 - 28.1 (23.9)" "2.4 - 42.8 (8.8)" 
[4] "1.1 - 48.8 (15.4)"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype4" "subtype4"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype4" "subtype4"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype4" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype4" "subtype4"
D7V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  0
  subtype3                  4
  subtype4                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
  subtype3                                                                                        5
  subtype4                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   6
  subtype2                   5
  subtype3                   6
  subtype4                  11
D7V3, multiclass
D7V4, binary
          cls
clus        0  1
  subtype1  5  4
  subtype2  2  4
  subtype3  4 11
  subtype4  5 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    4
  subtype2    2    4
  subtype3    4   11
  subtype4    5   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        5        2        4        5
  MALE          4        4       11       10
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1  7   0   0   0   0  1
  subtype2  3   0   1   1   0  1
  subtype3 10   1   3   0   0  0
  subtype4  7   2   0   0   2  3
D7V5, multiclass
D7V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       2        2        1        0         0         0
  subtype2           0       0        1        0        2         0         0
  subtype3           0       1        0        4        1         1         2
  subtype4           0       0        1        1        1         2         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          0          0          1        0
  subtype2         0         0          0          2          0        1
  subtype3         1         1          0          1          2        0
  subtype4         0         0          1          3          3        0
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 2 1
  subtype2 3 3
  subtype3 4 9
subtype1 subtype2 subtype3 
       3        6       13 
subtype1 subtype2 subtype3 
       1        3        9 
$subtype1
TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-EE-A2A2 
       28.08         5.39        23.90 

$subtype2
TCGA-D3-A2J8 TCGA-EE-A17X TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-ER-A19D TCGA-ER-A19N 
        8.38        11.57         8.12        25.28         3.52        42.84 

$subtype3
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L 
       16.47        48.79        39.19         7.00         4.27         1.08 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-GN-A267 
        8.84         9.99         2.43         8.09         9.67        16.21 
TCGA-GN-A268 
       15.39 

subtype1 subtype2 subtype3 
    5.39     3.52     1.08 
subtype1 subtype2 subtype3 
   28.08    42.84    48.79 
subtype1 subtype2 subtype3 
  23.900    9.975    9.670 
[1] "5.4 - 28.1 (23.9)" "3.5 - 42.8 (10.0)" "1.1 - 48.8 (9.7)" 
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype2" "subtype3" "subtype3"
D8V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  0
  subtype2                  1
  subtype3                  7
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        3
  subtype3                                                                                        5
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   4
  subtype2                   5
  subtype3                  19
D8V3, multiclass
D8V4, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2  3  6
  subtype3 11 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2    3    6
  subtype3   11   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        3       11
  MALE          3        6       20
          vv
clus       N0 N1A N1B N2A N2B N3
  subtype1  2   0   1   1   0  1
  subtype2  8   0   0   0   0  0
  subtype3 17   3   3   0   2  4
D8V5, multiclass
D8V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       0        1        0        1         0         0
  subtype2           0       1        1        3        0         0         1
  subtype3           1       2        2        3        3         3         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         0          0          2          0        1
  subtype2         2         0          0          0          0        0
  subtype3         0         1          1          4          6        0
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")
