
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-Regional_Metastatic/3157553/1.GDAC_mergedClustering.Finished/SKCM-Regional_Metastatic.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_Metastatic/3215667/SKCM-Regional_Metastatic.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=152, in cluster file=152, common to both=152
[1]   8 152
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
24 26 41 56 
 1  2  3  4 
24 26 41 56 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
43 57 52 
 1  2  3 
43 57 52 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
22 36 37 
 1  2  3 
22 36 37 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
16 26 34 19 
 1  2  3  4 
16 26 34 19 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
56 38 51 
 1  2  3 
56 38 51 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
48 64 33 
 1  2  3 
48 64 33 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
56 29 59 
 1  2  3 
56 29 59 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
32 18 94 
 1  2  3 
32 18 94 
[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 152 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
          NA           NA           NA         3687           NA           NA 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A148 
        2167           NA           NA           NA          653         4511 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
        1513           82          194          345           98         1487 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA         3564           NA         5926           NA           NA 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        1861           NA          713           NA          870           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A17Z 
        6553          477           28          309           NA           NA 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
          NA           NA           NA         3335         2399         1455 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
          NA         1205          979           NA           NA         1716 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        1136          440         1700        10523           NA           NA 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
        2401          743           NA         1787         1446         1315 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
        9567         4134         5536          686         2717         1664 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
        1673         2296         2766         3101           NA          435 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1691          595         2042           NA         3931           NA 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA         4403         6175           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
        7562           NA         3150         4150         1265         1620 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
         129         3733          786          112          813           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
         714           NA           NA           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
          NA         1340           NA         2433         2443         1010 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        2448         4885           NA           NA           NA           NA 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
          NA           NA           NA           NA         3080           NA 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 
          NA         4525         1505         2366           NA          378 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A261 
          NA         1504         2369          699           NA           NA 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        3664           NA         2577           NA           NA           NA 
TCGA-GN-A26A TCGA-GN-A26D 
          NA         1204 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=80,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=81,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "DISTANT.METASTASIS"     
[5] "LYMPH.NODE.METASTASIS"   "TUMOR.STAGECODE"        
[7] "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  6   4  11   3  17  15   6   4  19  10   4   7  20   1  12 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 152 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=10, 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 13 11
  subtype2 14 12
  subtype3 17 23
  subtype4 32 23
subtype1 subtype2 subtype3 subtype4 
      24       26       40       55 
subtype1 subtype2 subtype3 subtype4 
      11       12       23       23 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17Z 
       16.57         9.30         6.38       194.83        10.49         8.65 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GJ 
        4.93       109.64         2.56        14.47        55.89        89.33 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MN TCGA-EE-A3AB TCGA-EE-A3AD 
       90.94        14.30        67.13        47.54       122.73         3.68 
TCGA-ER-A19D TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-GN-A267 
       12.59        80.32        80.48        32.71        47.38        64.41 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D9-A148 TCGA-D9-A3Z3 
      112.54        31.59        71.24        21.47       148.31         3.22 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A29T TCGA-EE-A29X 
       36.03        61.18        53.92       215.44       345.96        17.92 
TCGA-EE-A2A6 TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MS 
       58.75        75.48       101.95       129.24        28.80       136.44 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19L TCGA-ER-A19M TCGA-FS-A1Z7 
       26.73        23.47       138.77       131.08        61.05         7.76 
TCGA-GN-A264 TCGA-GN-A26A 
      117.93        32.48 

$subtype3
TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A149 TCGA-D9-A1JW 
       71.80        43.40        58.03        60.23        49.74         2.70 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A181 
       48.89       117.17       176.55        35.93        68.09        33.73 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 
       78.87        13.97        32.19        56.42        37.35        39.25 
TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI 
       47.54        13.87        55.59        47.28        16.96       204.62 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N 
      144.76       248.61        13.81        26.37         6.41        44.05 
TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM 
       33.21       216.92        48.59        53.52         9.70       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A268 TCGA-GN-A26D 
       11.41       148.77        62.76        39.58 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      121.22        28.08        65.49        23.77        11.87        12.10 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       24.53        11.34        20.38        23.44        28.60        15.68 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A2A0 
       29.82        26.86        47.84        39.62        18.58        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       78.94        24.43        43.23       314.53       135.91       182.01 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 
       22.55        54.71        55.00        19.56        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       61.51       103.27       103.17        96.23       203.01       167.87 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       43.23       103.56        41.59        53.26         4.24        25.84 
TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A4F0 
       79.99       160.60        28.08        74.73        49.48        77.79 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 
       12.43        49.45        22.98        76.41       120.46        84.72 
TCGA-GN-A266 
       10.09 

subtype1 subtype2 subtype3 subtype4 
    2.56     3.22     2.70     4.24 
subtype1 subtype2 subtype3 subtype4 
  194.83   345.96   248.61   314.53 
subtype1 subtype2 subtype3 subtype4 
  40.045   61.115   48.065   43.230 
[1] "2.6 - 194.8 (40.0)" "3.2 - 346.0 (61.1)" "2.7 - 248.6 (48.1)"
[4] "4.2 - 314.5 (43.2)"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
  [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
 [13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype1" "subtype3" "subtype3"
 [31] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype1"
 [37] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype4"
 [49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [61] "subtype3" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [67] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
 [79] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [85] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [97] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype1"
[103] "subtype4" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[109] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[115] "subtype4" "subtype1" "subtype3" "subtype1" "subtype4" "subtype3"
[121] "subtype3" "subtype4" "subtype2" "subtype3" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
[133] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[139] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype2"
[145] "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
  [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
 [13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype1" "subtype3" "subtype3"
 [31] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype1"
 [37] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype4"
 [49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [61] "subtype3" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [67] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
 [79] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [85] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [97] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype1"
[103] "subtype4" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[109] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[115] "subtype4" "subtype1" "subtype3" "subtype1" "subtype4" "subtype3"
[121] "subtype3" "subtype4" "subtype2" "subtype3" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
[133] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[139] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype2"
[145] "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
  [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
 [13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype1" "subtype3" "subtype3"
 [31] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype1"
 [37] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype4"
 [49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype1"
 [55] "subtype1" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [61] "subtype3" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
 [67] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
 [79] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [85] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [97] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype1"
[103] "subtype4" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[109] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[115] "subtype4" "subtype1" "subtype3" "subtype1" "subtype4" "subtype3"
[121] "subtype3" "subtype4" "subtype2" "subtype3" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
[133] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[139] "subtype2" "subtype4" "subtype4" "subtype1" "subtype3" "subtype2"
[145] "subtype3"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  7 17
  subtype2  8 18
  subtype3 11 30
  subtype4  9 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   17
  subtype2    8   18
  subtype3   11   30
  subtype4    9   47
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        7
  REGIONAL LYMPH NODE                                                                            17
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        8
  REGIONAL LYMPH NODE                                                                            18
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       11
  REGIONAL LYMPH NODE                                                                            30
                                                                                          clus
vv                                                                                         subtype4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        9
  REGIONAL LYMPH NODE                                                                            47
D1V4, binary
          cls
clus        0  1
  subtype1 10 14
  subtype2 10 16
  subtype3 16 25
  subtype4 16 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   14
  subtype2   10   16
  subtype3   16   25
  subtype4   16   40
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       10       16       16
  MALE         14       16       25       40
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 21  0   0   0   1
  subtype2 22  0   0   1   0
  subtype3 36  1   1   0   0
  subtype4 49  0   1   1   0
D1V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 11  0   2   1  0   0   1   2  4  1
  subtype2 12  0   1   3  0   2   1   0  3  1
  subtype3 23  0   2   5  0   1   4   2  2  0
  subtype4 31  2   1   3  1   1   5   0  7  0
D1V6, multiclass
D1V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       2        2        2        2         2         1
  subtype2           1       1        2        2        4         0         0
  subtype3           0       2        1        4        7         1         4
  subtype4           0      11        3        5        4         4         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         1          2          1          5        1
  subtype2         2         0          1          5          3        0
  subtype3         2         3          1          5          4        2
  subtype4         0         4          1          5          9        1
D1V8, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 20 23
  subtype2 29 26
  subtype3 30 22
subtype1 subtype2 subtype3 
      43       55       52 
subtype1 subtype2 subtype3 
      23       26       22 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       16.57       112.54        43.40        71.24        60.23         9.30 
TCGA-D3-A3MV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EE-A17Z 
       21.47       176.55        61.18        10.49        10.16         8.65 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO 
      109.64        13.97        14.47        39.25        90.94       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MI TCGA-EE-A2MS 
       13.87        14.30        55.59        28.80       204.62       136.44 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3ET TCGA-ER-A3PL 
       41.59        25.84        12.59       131.08        80.32        33.21 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       48.59         7.76        53.52        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A267 
       11.41       148.77        26.73        77.88        22.98        64.41 
TCGA-GN-A26D 
       39.58 

$subtype2
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       71.80       121.22        28.08        65.49        23.77        11.87 
TCGA-D3-A3CF TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
       24.53        49.74         2.70        11.34         3.22        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       20.38        35.93        23.44        28.60       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29T 
       26.86        78.87        47.84        39.62        18.58       345.96 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82        78.94        58.75       314.53       135.91       182.01 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 
       22.55        54.71        55.00        19.56        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.17        16.96        96.23 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
      103.56        53.26         4.24        61.05        44.05        79.99 
TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A266 
      160.60        28.08        32.71        76.41        84.72        10.09 
TCGA-GN-A26A 
       32.48 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HV 
       31.59        12.10        58.03       148.31         6.38        48.89 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A17X 
      117.17       194.83        53.92        68.09         0.92        29.82 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q 
       33.73         4.93        32.19         2.56        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ 
       55.89        17.92        24.43        47.54        43.23        89.33 
TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       75.48        67.13       129.24       144.76       203.01       167.87 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       47.54       248.61        43.23       122.73         3.68        26.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-FR-A3YN 
       13.81        23.47       138.77        26.37         6.41        80.48 
TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 
      216.92         9.70        49.48        77.79        28.73        12.43 
TCGA-FS-A4FC TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       49.45       120.46       117.93        62.76 

subtype1 subtype2 subtype3 
    7.76     2.70     0.92 
subtype1 subtype2 subtype3 
  204.62   345.96   248.61 
subtype1 subtype2 subtype3 
   43.40    46.82    49.17 
[1] "7.8 - 204.6 (43.4)" "2.7 - 346.0 (46.8)" "0.9 - 248.6 (49.2)"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 16 27
  subtype2 10 47
  subtype3 10 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   27
  subtype2   10   47
  subtype3   10   42
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       16
  REGIONAL LYMPH NODE                                                                            27
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       10
  REGIONAL LYMPH NODE                                                                            47
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       10
  REGIONAL LYMPH NODE                                                                            42
D2V4, binary
          cls
clus        0  1
  subtype1 14 29
  subtype2 16 41
  subtype3 25 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   29
  subtype2   16   41
  subtype3   25   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       16       25
  MALE         29       41       27
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 39  0   1   0   0
  subtype2 50  0   1   1   1
  subtype3 44  1   0   1   0
D2V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 23  0   4   4  1   1   4   2  2  0
  subtype2 28  2   1   7  0   1   5   1  7  1
  subtype3 27  0   2   1  0   2   3   1  9  1
D2V6, multiclass
D2V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       2        0        4        8         2         3
  subtype2           0      10        3        5        5         3         1
  subtype3           0       4        5        5        4         2         4
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         2         5          2          5          6        1
  subtype2         0         4          1          7          8        2
  subtype3         2         0          2          5          9        1
D2V8, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 10 12
  subtype2 19 17
  subtype3 18 18
subtype1 subtype2 subtype3 
      22       36       36 
subtype1 subtype2 subtype3 
      12       17       18 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I8 
       16.57        71.80        65.49       117.17        35.93        53.92 
TCGA-DA-A1IB TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29T 
       23.44        78.87        47.84        39.62        14.47       345.96 
TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MP TCGA-EE-A2MU 
       46.82        13.87        21.67        61.51       248.61        53.26 
TCGA-ER-A19D TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       12.59        84.72        64.41        32.48 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-EE-A29P 
      112.54       121.22        28.08        60.23        48.89        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       24.43        54.71        55.00        19.56        67.13       129.24 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR 
      204.62        96.23       144.76       167.87        47.54       103.56 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
      136.44         4.24       122.73        25.84        26.73        13.81 
TCGA-EE-A3AG TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1Z4 
       23.47        26.37         6.41       131.08        44.05        28.08 
TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26D 
       53.52        32.71        47.38       117.93        10.09        39.58 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       31.59        43.40        11.87       148.31        49.74         2.70 
TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 
        6.38        36.03       176.55        68.09        29.82        33.73 
TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A2A6 
        4.93        32.19         2.56        18.58        55.89        58.75 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M8 
       43.23       182.01        22.55        14.30        55.59        19.76 
TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AD TCGA-ER-A1A1 TCGA-FS-A1YW 
       47.28       203.01        41.59         3.68        79.99       216.92 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A268 
        9.70       101.26        74.73        76.41       120.46        62.76 

subtype1 subtype2 subtype3 
   12.59     4.24     2.56 
subtype1 subtype2 subtype3 
  345.96   204.62   216.92 
subtype1 subtype2 subtype3 
  50.550   51.205   43.315 
[1] "12.6 - 346.0 (50.5)" "4.2 - 204.6 (51.2)"  "2.6 - 216.9 (43.3)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  7 15
  subtype2  2 34
  subtype3  6 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   15
  subtype2    2   34
  subtype3    6   31
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        7
  REGIONAL LYMPH NODE                                                                            15
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        2
  REGIONAL LYMPH NODE                                                                            34
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        6
  REGIONAL LYMPH NODE                                                                            31
D3V4, binary
          cls
clus        0  1
  subtype1  9 13
  subtype2 14 22
  subtype3 12 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   13
  subtype2   14   22
  subtype3   12   25
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       14       12
  MALE         13       22       25
          vv
clus       M0 M1 M1B M1C
  subtype1 21  0   0   0
  subtype2 23  1   1   1
  subtype3 34  0   1   0
D3V5, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1  9  0   3   3   0   2   0  3  1
  subtype2 21  0   0   2   0   1   1  2  0
  subtype3 18  2   0   4   2   2   2  4  1
D3V6, multiclass
D3V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       3        1        3        1         1         0
  subtype2           1       7        2        1        3         3         1
  subtype3           0       1        4        3        5         1         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         1          2          3          5        0
  subtype2         2         1          0          2          0        3
  subtype3         0         3          0          4          6        0
D3V8, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  6 10
  subtype2 12 14
  subtype3 16 17
  subtype4 13  6
subtype1 subtype2 subtype3 subtype4 
      16       26       33       19 
subtype1 subtype2 subtype3 subtype4 
      10       14       17        6 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-EE-A29C 
       16.57        71.80        65.49       117.17        35.93        47.84 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
       39.62        14.47        46.82        13.87        21.67        61.51 
TCGA-EE-A2MU TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       53.26        84.72        64.41        32.48 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-DA-A1I8 TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GL 
      112.54        28.08        53.92        55.89        24.43        55.00 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR 
       19.56       129.24       204.62       167.87        47.54       103.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19D 
        4.24       122.73        25.84        13.81        23.47        12.59 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZH 
       26.37         6.41        44.05        28.08        53.52        32.71 
TCGA-GN-A266 TCGA-GN-A26D 
       10.09        39.58 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A148 TCGA-D9-A149 TCGA-DA-A1I2 
       43.40        11.87        60.23       148.31        49.74       176.55 
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A2GC 
       68.09        29.82         4.93        32.19         2.56        43.23 
TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MK TCGA-EE-A2ML 
       22.55        14.30        55.59        47.28       144.76       203.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AE TCGA-ER-A19L TCGA-ER-A1A1 
      136.44        41.59         3.68        26.73       131.08        79.99 
TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-GN-A261 
      216.92         9.70        47.38       101.26        74.73        76.41 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
      120.46       117.93        62.76 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW 
      121.22        31.59         2.70         6.38        48.89        36.03 
TCGA-DA-A1IB TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       23.44        33.73        78.87        18.58        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MJ 
       58.75       182.01        54.71        67.13        19.76        96.23 
TCGA-EE-A2MP 
      248.61 

subtype1 subtype2 subtype3 subtype4 
   13.87     4.24     2.56     2.70 
subtype1 subtype2 subtype3 subtype4 
  117.17   204.62   216.92   345.96 
subtype1 subtype2 subtype3 subtype4 
  47.330   36.145   55.590   54.710 
[1] "13.9 - 117.2 (47.3)" "4.2 - 204.6 (36.1)"  "2.6 - 216.9 (55.6)" 
[4] "2.7 - 346.0 (54.7)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype3"
[19] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
[25] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype4"
[49] "subtype1" "subtype2" "subtype4" "subtype1" "subtype3" "subtype2"
[55] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
[61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype3"
[19] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
[25] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype4"
[49] "subtype1" "subtype2" "subtype4" "subtype1" "subtype3" "subtype2"
[55] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
[61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype3"
[19] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
[25] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype4"
[49] "subtype1" "subtype2" "subtype4" "subtype1" "subtype3" "subtype2"
[55] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
[61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[91] "subtype1" "subtype3" "subtype1" "subtype2"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  5 11
  subtype2  4 22
  subtype3  6 28
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   11
  subtype2    4   22
  subtype3    6   28
  subtype4    0   19
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        5
  REGIONAL LYMPH NODE                                                                            11
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        4
  REGIONAL LYMPH NODE                                                                            22
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        6
  REGIONAL LYMPH NODE                                                                            28
                                                                                          clus
vv                                                                                         subtype4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        0
  REGIONAL LYMPH NODE                                                                            19
D4V4, binary
          cls
clus        0  1
  subtype1  4 12
  subtype2  7 19
  subtype3 12 22
  subtype4 12  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   12
  subtype2    7   19
  subtype3   12   22
  subtype4   12    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        7       12       12
  MALE         12       19       22        7
          vv
clus       M0 M1 M1B M1C
  subtype1 15  0   0   0
  subtype2 15  1   1   1
  subtype3 29  0   1   0
  subtype4 19  0   0   0
D4V5, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1  6  0   3   3   0   1   0  2  0
  subtype2 14  0   0   1   0   0   1  3  0
  subtype3 17  1   0   4   0   2   2  4  0
  subtype4 11  1   0   1   2   2   0  0  2
D4V6, multiclass
D4V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       2        1        2        0         1         0
  subtype2           1       5        0        1        0         4         1
  subtype3           0       1        4        3        6         0         3
  subtype4           0       3        2        1        3         0         0
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         1          2          3          3        0
  subtype2         1         0          0          1          1        3
  subtype3         0         3          0          2          6        0
  subtype4         1         1          0          3          1        0
D4V8, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 25 31
  subtype2 24 13
  subtype3 25 25
subtype1 subtype2 subtype3 
      56       37       50 
subtype1 subtype2 subtype3 
      31       13       25 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.57       112.54        71.80        28.08        58.03        60.23 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.30        21.47         6.38       117.17       194.83       176.55 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29Q 
       61.18        53.92        10.49       215.44       109.64        37.35 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN 
       14.47       345.96        39.25       314.53       135.91        90.94 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      101.95        13.87        55.59        21.67       129.24        28.80 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       61.51       204.62       144.76       167.87       248.61       136.44 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19L 
      122.73        23.47       138.77        12.59         6.41       131.08 
TCGA-ER-A19M TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZH 
       61.05        33.21        48.59         7.76        53.52        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A261 TCGA-GN-A262 
      101.26        74.73        11.41       148.77        76.41       120.46 
TCGA-GN-A266 TCGA-GN-A26A 
       10.09        32.48 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1IB 
      121.22        65.49        23.77        24.53        48.89        23.44 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P 
       15.68        33.73        26.86        78.87        18.58        56.42 
TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GH 
       55.89        46.82        78.94        24.43        58.75       182.01 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME 
       22.55        54.71        55.00        19.56        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A3AA 
      103.17        16.96        96.23       203.01       103.56         4.24 
TCGA-EE-A3AE TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZW 
       26.73        44.05        79.99       160.60        28.08        49.48 
TCGA-GN-A265 
       84.72 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D9-A148 
       31.59        43.40        11.87        12.10        71.24       148.31 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I0 
       49.74         2.70        11.34         3.22        36.03        20.38 
TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C 
       35.93        68.09        29.82         8.65         4.93        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29X TCGA-EE-A2GB 
       13.97        39.62        32.19         2.56        17.92        47.54 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD 
       43.23        89.33        75.48        14.30        67.13        47.28 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD 
       47.54        43.23        41.59        53.26        25.84         3.68 
TCGA-EE-A3AF TCGA-ER-A19F TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       13.81        26.37        80.48       216.92         9.70        47.38 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 
       77.79        12.43        49.45        22.98       117.93        64.41 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

subtype1 subtype2 subtype3 
    6.38     4.24     2.56 
subtype1 subtype2 subtype3 
  345.96   203.01   216.92 
subtype1 subtype2 subtype3 
  61.115   49.480   39.600 
[1] "6.4 - 346.0 (61.1)" "4.2 - 203.0 (49.5)" "2.6 - 216.9 (39.6)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[115] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[115] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
 [19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[115] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 23 33
  subtype2  0 38
  subtype3 10 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   33
  subtype2    0   38
  subtype3   10   41
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       23
  REGIONAL LYMPH NODE                                                                            33
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        0
  REGIONAL LYMPH NODE                                                                            38
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       10
  REGIONAL LYMPH NODE                                                                            41
D5V4, binary
          cls
clus        0  1
  subtype1 22 34
  subtype2 12 26
  subtype3 17 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   34
  subtype2   12   26
  subtype3   17   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       12       17
  MALE         34       26       34
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 47  1   1   1   1
  subtype2 35  0   0   0   0
  subtype3 44  0   1   1   0
D5V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 28  1   2   4  0   1   3   3  7  2
  subtype2 25  1   1   2  0   0   3   0  3  0
  subtype3 24  0   2   6  1   3   4   1  6  0
D5V6, multiclass
D5V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       7        0        5        9         2         3
  subtype2           0       7        3        3        6         4         0
  subtype3           0       2        5        5        2         1         5
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         5          1          4          8        4
  subtype2         1         1          0          5          4        0
  subtype3         3         2          3          6          9        0
D5V8, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 20 28
  subtype2 41 22
  subtype3 13 19
subtype1 subtype2 subtype3 
      48       63       32 
subtype1 subtype2 subtype3 
      28       22       19 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3C6 
       16.57       112.54        71.80        28.08        65.49        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
       60.23         9.30        21.47       117.17       176.55        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A5 
       53.92       215.44       109.64        14.47        46.82        39.25 
TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91        90.94       101.95        55.59        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MR 
       28.80        61.51       204.62       144.76       167.87       103.56 
TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19L 
      136.44       122.73        23.47       138.77        12.59       131.08 
TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZH 
       33.21       216.92        48.59         7.76        53.52        32.71 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       74.73       148.77       120.46        84.72        10.09        32.48 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CF TCGA-D9-A148 
      121.22        31.59        23.77        11.87        24.53       148.31 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       49.74         2.70         6.38        11.34         3.22        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 
       36.03        20.38       194.83        23.44        10.49        15.68 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       33.73        26.86        78.87        32.19        18.58        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       37.35        55.89       345.96        17.92        78.94        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54        43.23       182.01        22.55        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD 
       54.71        55.00        19.56        67.13        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       103.17        16.96        96.23       203.01        47.54 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-ER-A19F 
      248.61        53.26         4.24        25.84        26.73        26.37 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z4 
       61.05        44.05        79.99        80.48       160.60        28.08 
TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-GN-A267 
       49.48        22.98        64.41 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3CC TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A17X 
       43.40        12.10        71.24        35.93        68.09        29.82 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        8.65         4.93        47.84        13.97        39.62         2.56 
TCGA-EE-A2GD TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MQ TCGA-EE-A2MT 
      314.53        75.48        13.87        14.30        43.23        41.59 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-ER-A19J TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        3.68        13.81         6.41         9.70        47.38       101.26 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-GN-A261 TCGA-GN-A264 
       11.41        77.79        12.43        49.45        76.41       117.93 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

subtype1 subtype2 subtype3 
    7.76     2.70     2.56 
subtype1 subtype2 subtype3 
  216.92   345.96   314.53 
subtype1 subtype2 subtype3 
   63.50    44.05    39.60 
[1] "7.8 - 216.9 (63.5)" "2.7 - 346.0 (44.0)" "2.6 - 314.5 (39.6)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[109] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 16 32
  subtype2  5 59
  subtype3 12 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   32
  subtype2    5   59
  subtype3   12   21
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       16
  REGIONAL LYMPH NODE                                                                            32
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        5
  REGIONAL LYMPH NODE                                                                            59
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       12
  REGIONAL LYMPH NODE                                                                            21
D6V4, binary
          cls
clus        0  1
  subtype1 17 31
  subtype2 20 44
  subtype3 14 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   31
  subtype2   20   44
  subtype3   14   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       20       14
  MALE         31       44       19
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 39  0   1   1   1
  subtype2 59  0   1   1   0
  subtype3 28  1   0   0   0
D6V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 27  0   1   4  0   1   2   2  5  0
  subtype2 35  1   3   6  1   2   4   0  7  2
  subtype3 15  1   1   2  0   1   4   2  4  0
D6V6, multiclass
D6V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       7        0        6        8         3         1
  subtype2           0       8        7        5        7         3         2
  subtype3           0       1        1        2        2         1         5
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         3          1          2          7        3
  subtype2         1         2          2          9          8        0
  subtype3         3         3          1          4          6        1
D6V8, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 29 27
  subtype2 17 11
  subtype3 27 31
subtype1 subtype2 subtype3 
      56       28       58 
subtype1 subtype2 subtype3 
      27       11       31 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       16.57        43.40        24.53       148.31        49.74         2.70 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB 
       11.34         3.22        48.89        36.03       176.55        23.44 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       68.09        10.49         8.65        33.73        26.86         4.93 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29X 
       78.87        13.97        39.62        32.19         2.56        17.92 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN 
       58.75        43.23        22.55        89.33        55.00        90.94 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       14.30        19.56        16.96        96.23       144.76       167.87 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       47.54        43.23       136.44        41.59         4.24        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A3PL TCGA-FR-A3YN 
        3.68        26.73        13.81       138.77        33.21        80.48 
TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A4F0 
      216.92         9.70        47.38        74.73        49.48        77.79 
TCGA-GN-A267 TCGA-GN-A268 
       64.41        62.76 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D9-A1JX 
      112.54        28.08        31.59        60.23        21.47         6.38 
TCGA-DA-A1I0 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A29P 
       20.38        53.92       215.44        15.68       109.64        56.42 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       46.82        24.43        47.54        67.13       129.24        28.80 
TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AG TCGA-ER-A19F 
       47.28       203.01       248.61       122.73        23.47        26.37 
TCGA-FS-A1ZH TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D 
       32.71       120.46        84.72        39.58 

$subtype3
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        65.49        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       58.03        71.24         9.30       117.17       194.83        35.93 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29N TCGA-EE-A29Q 
       61.18        28.60        29.82        47.84        18.58        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD 
       14.47        55.89       345.96        78.94        39.25       314.53 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
      135.91       182.01        54.71        75.48       101.95        13.87 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        21.67        19.76        61.51       103.27       103.17 
TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MU TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19L 
      204.62       103.56        53.26        12.59         6.41       131.08 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1YX TCGA-FS-A1Z4 
       61.05        44.05        79.99        80.32        48.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FW-A3R5 
        7.76        53.52       101.26        11.41       148.77        22.98 
TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
       76.41       117.93        10.09        32.48 

subtype1 subtype2 subtype3 
    2.56     6.38     6.41 
subtype1 subtype2 subtype3 
  216.92   248.61   345.96 
subtype1 subtype2 subtype3 
  40.605   47.410   55.740 
[1] "2.6 - 216.9 (40.6)" "6.4 - 248.6 (47.4)" "6.4 - 346.0 (55.7)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [85] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[127] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [85] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[127] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [85] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[127] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  6 50
  subtype2  6 23
  subtype3 22 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   50
  subtype2    6   23
  subtype3   22   37
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        6
  REGIONAL LYMPH NODE                                                                            50
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        6
  REGIONAL LYMPH NODE                                                                            23
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       22
  REGIONAL LYMPH NODE                                                                            37
D7V4, binary
          cls
clus        0  1
  subtype1 20 36
  subtype2 12 17
  subtype3 18 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   36
  subtype2   12   17
  subtype3   18   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       12       18
  MALE         36       17       41
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 50  0   1   1   0
  subtype2 21  0   1   1   1
  subtype3 54  1   0   0   0
D7V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 31  0   2   5  0   2   5   1  6  0
  subtype2 12  0   1   3  0   2   1   1  4  1
  subtype3 32  2   3   4  1   0   5   2  5  1
D7V6, multiclass
D7V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       4        5        4        9         3         5
  subtype2           1       2        1        0        4         1         0
  subtype3           0      10        2        9        3         2         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         0          2          7          9        1
  subtype2         2         1          1          5          3        2
  subtype3         2         7          2          4          8        1
D7V8, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 14 18
  subtype2 12  5
  subtype3 47 46
subtype1 subtype2 subtype3 
      32       17       93 
subtype1 subtype2 subtype3 
      18        5       46 
$subtype1
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1HY 
       71.80        65.49        23.77        11.87        60.23       117.17 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A29Q TCGA-EE-A29T 
       61.18        53.92       215.44        29.82        37.35       345.96 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC 
       54.71        75.48       101.95        21.67       129.24        61.51 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3AB TCGA-ER-A19D TCGA-ER-A19N 
      103.17       204.62       103.56       122.73        12.59        44.05 
TCGA-ER-A1A1 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZS TCGA-GN-A261 
       79.99        28.08        53.52        32.71       148.77        76.41 
TCGA-GN-A266 TCGA-GN-A26A 
       10.09        32.48 

$subtype2
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A3MV TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 
       28.08        31.59        21.47         6.38        20.38        28.60 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
       15.68       109.64        56.42        46.82        24.43        47.54 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AG TCGA-GN-A265 
       67.13        28.80       203.01        23.47        84.72 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 
       16.57       112.54       121.22        43.40        12.10        58.03 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       71.24        24.53         9.30       148.31        49.74         2.70 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.34         3.22        48.89        36.03       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 
       35.93        23.44        68.09        10.49         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.86         4.93        78.87        47.84        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X 
       32.19         2.56        18.58        14.47        55.89        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       78.94        39.25        58.75        43.23       314.53       135.91 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
      182.01        22.55        89.33        55.00        90.94        13.87 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       14.30        55.59        19.56        19.76        47.28       103.27 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96        96.23       144.76       167.87        47.54       248.61 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       43.23       136.44        41.59        53.26         4.24        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J 
        3.68        26.73        13.81       138.77        26.37         6.41 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YW 
      131.08        61.05        80.32        33.21        80.48       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       48.59         7.76         9.70        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 
       11.41        49.48        77.79        22.98       120.46       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       64.41        62.76        39.58 

subtype1 subtype2 subtype3 
   10.09     6.38     2.56 
subtype1 subtype2 subtype3 
  345.96   203.01   314.53 
subtype1 subtype2 subtype3 
  61.345   28.800   47.280 
[1] "10.1 - 346.0 (61.3)" "6.4 - 203.0 (28.8)"  "2.6 - 314.5 (47.3)" 
  [1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[127] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[139] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[127] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[139] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [91] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[127] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[139] "subtype3" "subtype3" "subtype1" "subtype3"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 10 22
  subtype2  5 13
  subtype3 19 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   22
  subtype2    5   13
  subtype3   19   75
                                                                                          clus
vv                                                                                         subtype1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       10
  REGIONAL LYMPH NODE                                                                            22
                                                                                          clus
vv                                                                                         subtype2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)        5
  REGIONAL LYMPH NODE                                                                            13
                                                                                          clus
vv                                                                                         subtype3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)       19
  REGIONAL LYMPH NODE                                                                            75
D8V4, binary
          cls
clus        0  1
  subtype1 11 21
  subtype2  6 12
  subtype3 33 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   21
  subtype2    6   12
  subtype3   33   61
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11        6       33
  MALE         21       12       61
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 28  0   0   0   1
  subtype2 14  0   1   1   0
  subtype3 83  1   1   1   0
D8V5, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 16  1   1   3  0   0   1   1  5  1
  subtype2  6  0   1   2  0   2   2   0  2  1
  subtype3 53  1   4   7  1   2   8   3  8  0
D8V6, multiclass
D8V7, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       7        1        2        2         1         2
  subtype2           0       0        1        0        3         1         0
  subtype3           1       9        6       11       11         4         6
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         3          1          1          6        1
  subtype2         1         0          1          6          1        1
  subtype3         2         5          3          9         13        2
D8V8, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"      "DISTANT.METASTASIS"   "LYMPH.NODE.METASTASIS" 
                       V7                        V8 
        "TUMOR.STAGECODE"   "NEOPLASM.DISEASESTAGE" 
> q(save="no")
