
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-NF1_Any_Mutants/3157448/1.GDAC_mergedClustering.Finished/SKCM-NF1_Any_Mutants.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NF1_Any_Mutants/3215659/SKCM-NF1_Any_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=25, in cluster file=31, common to both=25
[1]  8 25
[1] "CN_CNMF"
[1] 3
 1  2 
11 14 
 1  2 
11 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2 
10 15 
 1  2 
10 15 
[1] "RPPA_CNMF"
[1] 3
 1  2 
 6 15 
 1  2 
 6 15 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2 
 3 18 
 1  2 
 3 18 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
 5  9 11 
 1  2  3 
 5  9 11 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 
4 7 6 8 
1 2 3 4 
4 7 6 8 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2 
11 14 
 1  2 
11 14 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
1 4 2 4 8 6 
2 4 5 6 
4 4 8 6 
[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 25 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        1483           NA           NA           NA           NA           NA 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO 
          NA           NA           NA          743         1315         3101 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
         435           NA           NA         4150         1265          813 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
          NA           NA           NA           NA           NA            6 
TCGA-GN-A266 
          NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=12,	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=12,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	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
T1A T2A  T3 T3A T3B  T4 T4B  TX 
  3   1   2   2   4   2   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, 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=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 4 7
  subtype2 5 9
subtype1 subtype2 
      11       14 
subtype1 subtype2 
       7        9 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 
       48.76        20.38        29.82        33.73        18.58        24.43 
TCGA-EE-A2GC TCGA-EE-A2MJ TCGA-EE-A3AE TCGA-FS-A1ZP TCGA-GN-A266 
       43.23        96.23        26.73        74.73        10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2GO TCGA-EE-A2GR 
       68.09        14.70         2.56        25.87       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      204.62       136.44        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.02         0.20 

subtype1 subtype2 
   10.09     0.20 
subtype1 subtype2 
   96.23   204.62 
subtype1 subtype2 
  29.820   26.695 
[1] "10.1 - 96.2 (29.8)" "0.2 - 204.6 (26.7)"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype1"
[1] "hr=" "1.1"
D1V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  1
  subtype2                  6
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   8
  subtype2                   5
D1V3, multiclass
D1V4, binary
          cls
clus       0 1
  subtype1 2 9
  subtype2 6 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    9
  subtype2    6    8
        clus
vv       subtype1 subtype2
  FEMALE        2        6
  MALE          9        8
          vv
clus       N0 N1B N2C N3
  subtype1  8   1   0  1
  subtype2  8   2   2  1
D1V5, multiclass
D1V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        3        0        3         1          1          1        0
  subtype2        0        1        3         2          2          3        1
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 7
  subtype2 6 9
subtype1 subtype2 
      10       15 
subtype1 subtype2 
       7        9 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2MI 
       48.76        20.38        33.73        18.58        25.87       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-GN-A266 
       96.23       136.44        41.59        10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GC 
       68.09        29.82        14.70         2.56        24.43        43.23 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      101.95        14.30        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       74.73        27.02         0.20 

subtype1 subtype2 
   10.09     0.20 
subtype1 subtype2 
  204.62   101.95 
subtype1 subtype2 
   37.66    26.73 
[1] "10.1 - 204.6 (37.7)" "0.2 - 102.0 (26.7)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype1"
[1] "hr=" "1.5"
D2V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  5
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   6
  subtype2                   7
D2V3, multiclass
D2V4, binary
          cls
clus       0 1
  subtype1 1 9
  subtype2 7 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    7    8
        clus
vv       subtype1 subtype2
  FEMALE        1        7
  MALE          9        8
          vv
clus       N0 N1B N2C N3
  subtype1  7   1   0  1
  subtype2  9   2   2  1
D2V5, multiclass
D2V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        1        1        3         1          0          2        0
  subtype2        2        0        3         2          3          2        1
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 0 6
  subtype2 6 9
subtype1 subtype2 
       6       15 
subtype1 subtype2 
       6        9 
$subtype1
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V TCGA-FS-A1ZA TCGA-FS-A1ZZ 
       68.09        14.70        18.58        25.87        27.68        27.02 

$subtype2
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
       29.82        33.73         2.56        24.43        43.23        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F 
      204.62        96.23       136.44        41.59        26.73        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-GN-A266 
       20.91        74.73        10.09 

subtype1 subtype2 
   14.70     2.56 
subtype1 subtype2 
   68.09   204.62 
subtype1 subtype2 
  26.445   29.820 
[1] "14.7 - 68.1 (26.4)" "2.6 - 204.6 (29.8)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype1" "subtype2"
[1] "hr=" "3.3"
D3V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  4
  subtype2                  1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   1
  subtype2                  12
D3V3, multiclass
D3V4, binary
          cls
clus        0  1
  subtype1  3  3
  subtype2  3 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    3   12
        clus
vv       subtype1 subtype2
  FEMALE        3        3
  MALE          3       12
          vv
clus       N0 N1B N2C N3
  subtype1  2   2   2  0
  subtype2 11   1   0  1
D3V5, multiclass
D3V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  subtype1        0        0        0         1          2          2
  subtype2        2        1        5         2          1          1
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  0  3
  subtype2  6 12
subtype1 subtype2 
       3       18 
subtype1 subtype2 
       3       12 
$subtype1
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29V 
       68.09        14.70        25.87 

$subtype2
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC 
       29.82        33.73         2.56        18.58        24.43        43.23 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       14.30       204.62        96.23       136.44        41.59        26.73 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       26.37        20.91        27.68        74.73        27.02        10.09 

subtype1 subtype2 
   14.70     2.56 
subtype1 subtype2 
   68.09   204.62 
subtype1 subtype2 
   25.87    27.35 
[1] "14.7 - 68.1 (25.9)" "2.6 - 204.6 (27.4)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2"
[1] "hr=" "2.3"
D4V2, 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                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   0
  subtype2                  13
D4V3, multiclass
D4V4, binary
          cls
clus        0  1
  subtype1  1  2
  subtype2  5 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    5   13
        clus
vv       subtype1 subtype2
  FEMALE        1        5
  MALE          2       13
          vv
clus       N0 N1B N2C N3
  subtype1  0   2   1  0
  subtype2 13   1   1  1
D4V5, multiclass
D4V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  subtype1        0        0        0         0          1          2
  subtype2        2        1        5         3          2          1
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 2 3
  subtype2 4 5
  subtype3 3 8
subtype1 subtype2 subtype3 
       5        9       11 
subtype1 subtype2 subtype3 
       3        5        8 
$subtype1
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MS TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      101.95       204.62       136.44        20.91        27.68 

$subtype2
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MJ 
       48.76        33.73        18.58        24.43        43.23        96.23 
TCGA-EE-A3AE TCGA-FS-A1ZP TCGA-GN-A266 
       26.73        74.73        10.09 

$subtype3
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       20.38        68.09        29.82        14.70         2.56        25.87 
TCGA-EE-A2GR TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZZ TCGA-FW-A3I3 
       14.30        41.59        26.37        27.02         0.20 

subtype1 subtype2 subtype3 
   20.91    10.09     0.20 
subtype1 subtype2 subtype3 
  204.62    96.23    68.09 
subtype1 subtype2 subtype3 
  101.95    33.73    25.87 
[1] "20.9 - 204.6 (102.0)" "10.1 - 96.2 (33.7)"   "0.2 - 68.1 (25.9)"   
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype2"
D5V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  1
  subtype3                  4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
  subtype3                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   2
  subtype2                   7
  subtype3                   4
D5V3, multiclass
D5V4, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 2 7
  subtype3 3 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    2    7
  subtype3    3    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        2        3
  MALE          2        7        8
          vv
clus       N0 N1B N2C N3
  subtype1  3   0   1  0
  subtype2  7   1   0  0
  subtype3  6   2   1  2
D5V5, multiclass
D5V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        0        0        2         1          1          0        0
  subtype2        2        0        3         1          1          0        0
  subtype3        1        1        1         1          1          4        1
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 1 3
  subtype2 3 4
  subtype3 1 5
  subtype4 4 4
subtype1 subtype2 subtype3 subtype4 
       4        7        6        8 
subtype1 subtype2 subtype3 subtype4 
       3        4        5        4 
$subtype1
TCGA-D3-A2JF TCGA-EE-A2MI TCGA-FS-A1ZA TCGA-GN-A266 
       48.76       204.62        27.68        10.09 

$subtype2
TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MJ TCGA-EE-A3AE 
       33.73        18.58        24.43        43.23        96.23        26.73 
TCGA-FS-A1ZP 
       74.73 

$subtype3
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-FW-A3I3 
       20.38        68.09        29.82        14.70        25.87         0.20 

$subtype4
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F 
        2.56       101.95        14.30       136.44        41.59        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZZ 
       20.91        27.02 

subtype1 subtype2 subtype3 subtype4 
   10.09    18.58     0.20     2.56 
subtype1 subtype2 subtype3 subtype4 
  204.62    96.23    68.09   136.44 
subtype1 subtype2 subtype3 subtype4 
  38.220   33.730   23.125   26.695 
[1] "10.1 - 204.6 (38.2)" "18.6 - 96.2 (33.7)"  "0.2 - 68.1 (23.1)"  
[4] "2.6 - 136.4 (26.7)" 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
[19] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype3"
[25] "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
[19] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype3"
[25] "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype2" "subtype4"
[13] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype2"
[19] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype3"
[25] "subtype1"
D6V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  0
  subtype3                  3
  subtype4                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        0
  subtype3                                                                                        2
  subtype4                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   1
  subtype2                   7
  subtype3                   1
  subtype4                   4
D6V3, multiclass
D6V4, binary
          cls
clus       0 1
  subtype1 1 3
  subtype2 2 5
  subtype3 2 4
  subtype4 3 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    2    5
  subtype3    2    4
  subtype4    3    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        2        3
  MALE          3        5        4        5
          vv
clus       N0 N1B N2C N3
  subtype1  2   0   1  0
  subtype2  6   1   0  0
  subtype3  2   2   1  1
  subtype4  6   0   0  1
D6V5, multiclass
D6V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        1        0        0         1          1          0        0
  subtype2        1        0        3         1          1          0        0
  subtype3        1        0        0         0          1          3        1
  subtype4        0        1        3         1          0          1        0
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 3 8
  subtype2 6 8
subtype1 subtype2 
      11       14 
subtype1 subtype2 
       8        8 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
       48.76        20.38        29.82        14.70        18.58        25.87 
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-FS-A1ZA TCGA-FW-A3I3 TCGA-GN-A266 
      101.95       204.62        27.68         0.20        10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
       68.09        33.73         2.56        24.43        43.23        14.30 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
       96.23       136.44        41.59        26.73        26.37        20.91 
TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       74.73        27.02 

subtype1 subtype2 
    0.20     2.56 
subtype1 subtype2 
  204.62   136.44 
subtype1 subtype2 
  25.870   30.375 
[1] "0.2 - 204.6 (25.9)" "2.6 - 136.4 (30.4)"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[25] "subtype1"
[1] "hr=" "1.4"
D7V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  5
  subtype2                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        3
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   3
  subtype2                  10
D7V3, multiclass
D7V4, binary
          cls
clus        0  1
  subtype1  4  7
  subtype2  4 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    7
  subtype2    4   10
        clus
vv       subtype1 subtype2
  FEMALE        4        4
  MALE          7       10
          vv
clus       N0 N1B N2C N3
  subtype1  6   2   1  1
  subtype2 10   1   1  1
D7V5, multiclass
D7V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        2        0        1         1          1          3        1
  subtype2        1        1        5         2          2          1        0
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype2 1 3
  subtype4 2 2
  subtype5 2 6
  subtype6 3 3
subtype2 subtype4 subtype5 subtype6 
       4        4        8        6 
subtype2 subtype4 subtype5 subtype6 
       3        2        6        3 
$subtype2
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-FS-A1ZA TCGA-GN-A266 
      101.95       204.62        27.68        10.09 

$subtype4
TCGA-DA-A1I0 TCGA-EE-A182 TCGA-EE-A2A2 TCGA-FW-A3I3 
       20.38        14.70        24.43         0.20 

$subtype5
TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
       33.73         2.56        43.23        26.73        26.37        20.91 
TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       74.73        27.02 

$subtype6
TCGA-DA-A1IC TCGA-EE-A29V TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT 
       68.09        25.87        14.30        96.23       136.44        41.59 

subtype2 subtype4 subtype5 subtype6 
   10.09     0.20     2.56    14.30 
subtype2 subtype4 subtype5 subtype6 
  204.62    24.43    74.73   136.44 
subtype2 subtype4 subtype5 subtype6 
  64.815   17.540   26.875   54.840 
[1] "10.1 - 204.6 (64.8)" "0.2 - 24.4 (17.5)"   "2.6 - 74.7 (26.9)"  
[4] "14.3 - 136.4 (54.8)"
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype2" "subtype6" "subtype2" "subtype6"
[13] "subtype6" "subtype6" "subtype5" "subtype5" "subtype5" "subtype2"
[19] "subtype5" "subtype5" "subtype4" "subtype2"
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype2" "subtype6" "subtype2" "subtype6"
[13] "subtype6" "subtype6" "subtype5" "subtype5" "subtype5" "subtype2"
[19] "subtype5" "subtype5" "subtype4" "subtype2"
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype2" "subtype6" "subtype2" "subtype6"
[13] "subtype6" "subtype6" "subtype5" "subtype5" "subtype5" "subtype2"
[19] "subtype5" "subtype5" "subtype4" "subtype2"
D8V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype2                  1
  subtype4                  2
  subtype5                  2
  subtype6                  1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype2                                                                                        2
  subtype4                                                                                        1
  subtype5                                                                                        0
  subtype6                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype2                   1
  subtype4                   1
  subtype5                   6
  subtype6                   3
D8V3, multiclass
D8V4, binary
          cls
clus       0 1
  subtype2 2 2
  subtype4 2 2
  subtype5 4 4
  subtype6 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    2
  subtype4    2    2
  subtype5    4    4
  subtype6    0    6
        clus
vv       subtype2 subtype4 subtype5 subtype6
  FEMALE        2        2        4        0
  MALE          2        2        4        6
          vv
clus       N0 N1B N2C N3
  subtype2  2   0   1  0
  subtype4  1   2   0  1
  subtype5  6   0   0  1
  subtype6  4   1   1  0
D8V5, multiclass
D8V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype2        0        0        1         1          1          0        0
  subtype4        0        0        0         0          1          2        1
  subtype5        1        0        2         2          0          1        0
  subtype6        0        1        3         0          1          1        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")
