
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-All_Samples/3161161/1.GDAC_mergedClustering.Finished/SKCM-All_Samples.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Samples/3215655/SKCM-All_Samples.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=211, in cluster file=316, common to both=211
[1]   8 211
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
43 65 40 54 
 1  2  3  4 
43 65 40 54 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
56 78 77 
 1  2  3 
56 78 77 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
57 31 33 
 1  2  3 
57 31 33 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
36 55 30 
 1  2  3 
36 55 30 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
32 56 60 50 
 1  2  3  4 
32 56 60 50 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
59 77 62 
 1  2  3 
59 77 62 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
87 57 53 
 1  2  3 
87 57 53 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2 
126  71 
  1   2 
126  71 
[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 211 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         3004           NA           NA 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK 
          NA           NA           NA           NA          939           NA 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
          NA         1390           NA           NA           NA          164 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
          NA           NA           NA           NA           NA          122 
TCGA-D9-A3Z3 TCGA-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
          87          118         1484           NA         1555           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        1192           NA           NA         1354         1116           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          680           NA          589           NA          534 
TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 TCGA-EB-A3HV 
         451           16           13           41           NA           39 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF TCGA-EB-A3Y6 
          36            9           NA           NA            4           16 
TCGA-EB-A3Y7 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EB-A430 
          NA            8            3            6           12           NA 
TCGA-EB-A431 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A4IQ TCGA-EE-A17X TCGA-EE-A17Z 
          52            6            6            4           NA           NA 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
          NA           NA           NA           NA         1097          156 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
          NA           NA         1155           NA         1175          134 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
          NA          825           NA          366          247          269 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
         304          197           NA           NA           NA          769 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
         727           NA          272           NA           NA           NA 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS 
        1303           NA         2386          200           52           NA 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
         307          181           NA         2195           NA           NA 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZN TCGA-FS-A1ZP 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
          NA           NA         1637           NA           NA           NA 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
          NA          328           NA          195           69            6 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A2C7 TCGA-GN-A261 TCGA-GN-A262 
          31            4           NA           NA           NA          756 
TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
          NA           NA         2577           NA           NA           NA 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-HR-A2OG TCGA-HR-A2OH 
          NA           NA           NA          447           NA           NA 
TCGA-IH-A3EA 
         383 
Variable 1:'AGE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=95,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	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=FALSE.
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"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "GENDER"                                
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "DISTANT.METASTASIS"                    
[6] "LYMPH.NODE.METASTASIS"                 
[7] "TUMOR.STAGECODE"                       
[8] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  6   5  14   3  20  18   7   4  24  14   6   8  51   1  14 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 211 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=67, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, 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 14 12
  subtype2 18 18
  subtype3 11  8
  subtype4 16 17
subtype1 subtype2 subtype3 subtype4 
      26       36       19       33 
subtype1 subtype2 subtype3 subtype4 
      12       18        8       17 
$subtype1
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A3Z1 
       70.16        28.08         6.35        45.70        24.00         4.01 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EE-A17X 
       13.68        44.52         0.43         1.28         0.30        11.57 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29P TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A2OS 
        5.13        38.63        12.03        12.99        28.64        12.10 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-GN-A262 TCGA-GN-A263 
       72.16        53.82        10.78         6.41        24.85        15.35 
TCGA-GN-A266 TCGA-GN-A269 
       10.09         5.59 

$subtype2
TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A3Z4 TCGA-DA-A1HY 
       10.26        30.87        15.25        13.32         3.88        51.12 
TCGA-DA-A1I1 TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A24D TCGA-EB-A3XF TCGA-EB-A3Y6 
       39.19         6.64         7.00         1.35         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
        0.26         0.10         0.39         1.12         4.27        36.07 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A5 
        7.96        11.15         8.84         9.99         2.43         9.67 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A3ET TCGA-ER-A3PL 
        3.52        11.11         4.18        42.84         6.58         1.71 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A26D 
       24.00         8.81         3.22         0.13        15.39        14.70 

$subtype3
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       98.76         8.38        21.14        22.36        19.36        14.83 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29N TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        1.35        12.20         9.47        11.31        25.28        23.90 
TCGA-ER-A1A1 TCGA-FR-A3R1 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A26C 
       78.44        10.09         1.02        15.35        84.72        24.00 
TCGA-IH-A3EA 
       12.59 

$subtype4
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO TCGA-D3-A3MV 
       16.47        32.55        22.55        11.41         9.30         5.39 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I7 
        2.86        48.79        35.80        10.03         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A42Y 
       25.15         4.93        17.56         0.53         1.18         0.20 
TCGA-EE-A17Z TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        6.31         8.81        37.97         4.41         1.08        27.12 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A6 TCGA-FR-A3YN TCGA-FW-A3I3 
        8.12         6.48         8.09         8.94         5.95         0.20 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
       31.33        16.21        12.16 

subtype1 subtype2 subtype3 subtype4 
    0.30     0.10     1.02     0.20 
subtype1 subtype2 subtype3 subtype4 
   72.16    51.12    98.76    48.79 
subtype1 subtype2 subtype3 subtype4 
  12.545    7.480   15.350    9.300 
[1] "0.3 - 72.2 (12.5)" "0.1 - 51.1 (7.5)"  "1.0 - 98.8 (15.3)"
[4] "0.2 - 48.8 (9.3)" 
  [1] "subtype4" "subtype4" "subtype1" "subtype3" "subtype1" "subtype4"
  [7] "subtype2" "subtype3" "subtype3" "subtype4" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype4" "subtype4"
 [19] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [25] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [31] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype2"
 [37] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype1"
 [43] "subtype4" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype2" "subtype1" "subtype4" "subtype4" "subtype4"
 [67] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype4" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype4" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype4" "subtype3" "subtype1" "subtype4"
[109] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
  [1] "subtype4" "subtype4" "subtype1" "subtype3" "subtype1" "subtype4"
  [7] "subtype2" "subtype3" "subtype3" "subtype4" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype4" "subtype4"
 [19] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [25] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [31] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype2"
 [37] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype1"
 [43] "subtype4" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype2" "subtype1" "subtype4" "subtype4" "subtype4"
 [67] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype4" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype4" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype4" "subtype3" "subtype1" "subtype4"
[109] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
  [1] "subtype4" "subtype4" "subtype1" "subtype3" "subtype1" "subtype4"
  [7] "subtype2" "subtype3" "subtype3" "subtype4" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype4" "subtype4"
 [19] "subtype1" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [25] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [31] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype2"
 [37] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype1"
 [43] "subtype4" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype2" "subtype1" "subtype4" "subtype4" "subtype4"
 [67] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype4" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype4" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype4" "subtype3" "subtype1" "subtype4"
[109] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
D1V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  6             8
  subtype2                 11             8
  subtype3                  4             5
  subtype4                  6             5
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        8
  subtype2                                                                                       14
  subtype3                                                                                        4
  subtype4                                                                                       11
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  21
  subtype2                  32
  subtype3                  27
  subtype4                  32
D1V3, multiclass
D1V4, binary
          cls
clus        0  1
  subtype1 17 26
  subtype2 24 41
  subtype3 13 27
  subtype4 22 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   26
  subtype2   24   41
  subtype3   13   27
  subtype4   22   32
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       24       13       22
  MALE         26       41       27       32
D1V5, binary
          cls
clus        0  1
  subtype1  1 42
  subtype2  0 65
  subtype3  2 38
  subtype4  0 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   42
  subtype2    0   65
  subtype3    2   38
  subtype4    0   54
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        2        0
  YES       42       65       38       54
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 34  0   0   1   2
  subtype2 57  1   1   0   0
  subtype3 38  0   0   0   0
  subtype4 47  1   1   1   1
D1V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 24  0   0   2  0   1   4   0  6  1
  subtype2 36  0   5   8  0   1   3   2  5  0
  subtype3 23  2   1   2  1   0   4   2  2  1
  subtype4 27  0   2   5  0   3   3   2  6  3
D1V7, multiclass
D1V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       2        2        2        5         3         3
  subtype2           2       3        3        5        8         3         3
  subtype3           0       8        1        4        2         3         2
  subtype4           1       4        4        4        5         0         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         6         2          0          2          6        3
  subtype2         7         3          4          5          9        2
  subtype3         3         3          0          6          5        0
  subtype4         7         1          3          8          7        2
D1V9, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 15 19
  subtype2 26 19
  subtype3 23 21
subtype1 subtype2 subtype3 
      34       45       44 
subtype1 subtype2 subtype3 
      19       19       21 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       16.47        32.55        10.26        45.70        13.32         9.30 
TCGA-D9-A3Z4 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A24C TCGA-EB-A24D 
        3.88        13.68         4.93         7.00         0.43         1.35 
TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A44R TCGA-EB-A4IQ TCGA-EE-A17Z TCGA-EE-A182 
        0.53         0.10         0.20         0.13         6.31         1.35 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L 
        8.81        11.15         8.84         9.67         3.52        12.99 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FS-A1ZR TCGA-FS-A4FB TCGA-FS-A4FD 
        6.58         1.71        12.10         8.81         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A26D 
        0.20         0.13        16.21        14.70 

$subtype2
TCGA-D3-A1Q9 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MV TCGA-DA-A1HV 
       22.55        30.87         6.35        15.25         5.39        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A3HV 
       51.12        39.19        36.69        25.15         6.64         1.28 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EB-A44Q 
        0.30         0.13         0.26         0.20         0.39         0.20 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29L 
       11.57         1.12         4.27         7.96         4.41         1.08 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-ER-A19F 
       12.03         8.12         9.99         8.09        23.90        11.11 
TCGA-ER-A19J TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F2 
        4.18        10.09         5.95        24.00        53.82         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A262 
        7.36        28.73        10.78         6.41         1.02        24.85 
TCGA-GN-A264 TCGA-GN-A268 TCGA-IH-A3EA 
       31.33        15.39        12.59 

$subtype3
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       70.16        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 
       24.00         4.01         2.86        35.80        10.03         9.99 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK 
       44.52        22.36        19.36        17.56        14.83         0.53 
TCGA-EB-A3XB TCGA-EB-A431 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
        1.18         1.71        12.20        36.07         5.13        37.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
       38.63        27.12         9.47         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A 
       25.28         8.94        28.64        42.84        78.44        72.16 
TCGA-FS-A4F8 TCGA-GN-A261 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A269 
       14.20        15.35        15.35        84.72        10.09         5.59 
TCGA-GN-A26A TCGA-GN-A26C 
       12.16        24.00 

subtype1 subtype2 subtype3 
    0.10     0.13     0.53 
subtype1 subtype2 subtype3 
   45.70    53.82    98.76 
subtype1 subtype2 subtype3 
    6.79     8.12    15.35 
[1] "0.1 - 45.7 (6.8)"  "0.1 - 53.8 (8.1)"  "0.5 - 98.8 (15.3)"
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [43] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype1" "subtype2"
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [43] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype1" "subtype2"
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [19] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [43] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[121] "subtype3" "subtype1" "subtype2"
D2V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 11             8
  subtype2                 11            10
  subtype3                  7            10
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                       11
  subtype2                                                                                       16
  subtype3                                                                                       11
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  26
  subtype2                  41
  subtype3                  49
D2V3, multiclass
D2V4, binary
          cls
clus        0  1
  subtype1 23 33
  subtype2 34 44
  subtype3 23 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   33
  subtype2   34   44
  subtype3   23   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       34       23
  MALE         33       44       54
D2V5, binary
          cls
clus        0  1
  subtype1  0 56
  subtype2  1 77
  subtype3  2 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   56
  subtype2    1   77
  subtype3    2   75
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        2
  YES       56       77       75
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 49  1   1   0   0
  subtype2 69  1   0   1   0
  subtype3 67  0   1   1   3
D2V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 32  1   4   6  0   0   4   1  3  1
  subtype2 45  0   3   2  1   3   5   3  9  1
  subtype3 37  2   2   9  0   2   6   2  9  3
D2V7, multiclass
D2V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       3        1        4        6         3         5
  subtype2           3       4        6        6        5         4         4
  subtype3           0      11        3        6        9         3         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         8         3          2          6          8        2
  subtype2        12         2          4          7         10        1
  subtype3         4         5          1         10         11        4
D2V9, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 11 11
  subtype2  4 12
  subtype3  9 14
subtype1 subtype2 subtype3 
      22       16       23 
subtype1 subtype2 subtype3 
      11       12       14 
$subtype1
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-EB-A24D 
       32.55        98.76        22.55        13.32        48.79         1.35 
TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2A6 
        1.12        27.12        12.03         9.99        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZN TCGA-GN-A262 
       11.11         4.18        12.99        42.84        24.00        24.85 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26C TCGA-GN-A26D 
       31.33        10.09        24.00        14.70 

$subtype2
TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.26        11.41        35.80        13.68         4.93        22.36 
TCGA-DA-A1IC TCGA-EB-A24C TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L 
        6.64         0.43        11.57         4.27         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-ER-A1A1 TCGA-GN-A268 
        9.47         2.43        78.44        15.39 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I4 
       16.47        70.16        28.08         8.38        51.12         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EB-A1NK TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29C 
       44.52        25.15         0.53         1.35         5.13        37.97 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A0 TCGA-ER-A19D TCGA-GN-A261 
       38.63         8.84         6.48        11.31         3.52        15.35 
TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A 
       15.35        84.72        16.21         5.59        12.16 

subtype1 subtype2 subtype3 
    1.12     0.43     0.53 
subtype1 subtype2 subtype3 
   98.76    78.44    84.72 
subtype1 subtype2 subtype3 
  18.625    9.865   15.350 
[1] "1.1 - 98.8 (18.6)" "0.4 - 78.4 (9.9)"  "0.5 - 84.7 (15.3)"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
D3V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  5             4
  subtype2                  5             1
  subtype3                  5             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        3
  subtype2                                                                                        5
  subtype3                                                                                        9
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  45
  subtype2                  20
  subtype3                  15
D3V3, multiclass
D3V4, binary
          cls
clus        0  1
  subtype1 23 34
  subtype2  9 22
  subtype3 14 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   34
  subtype2    9   22
  subtype3   14   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23        9       14
  MALE         34       22       19
D3V5, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  2 29
  subtype3  0 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    2   29
  subtype3    0   33
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        0
  YES       56       29       33
          vv
clus       M0 M1 M1B M1C
  subtype1 44  1   0   1
  subtype2 27  0   1   0
  subtype3 28  0   1   2
D3V6, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1 34  1   1   3   2   3   1  1  1
  subtype2 11  0   0   6   1   4   2  4  1
  subtype3 14  1   3   4   0   1   1  6  1
D3V7, multiclass
D3V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           2       7        4        5        6         4         2
  subtype2           1       1        3        0        3         0         2
  subtype3           0       3        1        4        1         1         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         3         3          1          5          1        2
  subtype2         1         1          0          4          8        0
  subtype3         2         2          2          4          6        3
D3V9, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  9  7
  subtype2  8 17
  subtype3  7 13
subtype1 subtype2 subtype3 
      16       25       20 
subtype1 subtype2 subtype3 
       7       17       13 
$subtype1
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-DA-A1I8 TCGA-EB-A24D 
       32.55        98.76        28.08        48.79        25.15         1.35 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F 
       12.03         9.99         6.48        23.90         3.52        11.11 
TCGA-ER-A19N TCGA-GN-A266 TCGA-GN-A26C TCGA-GN-A26D 
       42.84        10.09        24.00        14.70 

$subtype2
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1IA 
       22.55        10.26        11.41        13.32        35.80         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EB-A24C TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 
       22.36         6.64         0.43        11.57         1.12         4.27 
TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2A6 
        5.13         4.41         1.08        27.12         9.47         8.94 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FS-A1ZN TCGA-GN-A262 TCGA-GN-A264 
        4.18        12.99        78.44        24.00        24.85        31.33 
TCGA-GN-A268 
       15.39 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
       16.47        70.16         8.38        51.12        13.68         9.99 
TCGA-DA-A1I5 TCGA-EB-A1NK TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29R 
       44.52         0.53         1.35        37.97        38.63         8.84 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-GN-A261 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A267 
        2.43        11.31        15.35        15.35        84.72        16.21 
TCGA-GN-A269 TCGA-GN-A26A 
        5.59        12.16 

subtype1 subtype2 subtype3 
    1.35     0.43     0.53 
subtype1 subtype2 subtype3 
   98.76    78.44    84.72 
subtype1 subtype2 subtype3 
  19.300   11.410   14.515 
[1] "1.4 - 98.8 (19.3)" "0.4 - 78.4 (11.4)" "0.5 - 84.7 (14.5)"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
 [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[37] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[43] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[61] "subtype1"
D4V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2             2
  subtype2                  7             3
  subtype3                  6             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        4
  subtype2                                                                                        6
  subtype3                                                                                        7
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  28
  subtype2                  39
  subtype3                  13
D4V3, multiclass
D4V4, binary
          cls
clus        0  1
  subtype1 14 22
  subtype2 22 33
  subtype3 10 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   22
  subtype2   22   33
  subtype3   10   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       22       10
  MALE         22       33       20
D4V5, binary
          cls
clus        0  1
  subtype1  1 35
  subtype2  2 53
  subtype3  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   35
  subtype2    2   53
  subtype3    0   30
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        0
  YES       35       53       30
          vv
clus       M0 M1 M1B M1C
  subtype1 26  0   1   1
  subtype2 47  1   1   0
  subtype3 26  0   0   2
D4V6, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1 21  0   0   1   0   3   1  2  1
  subtype2 27  1   1   6   3   3   2  5  2
  subtype3 11  1   3   6   0   2   1  4  0
D4V7, multiclass
D4V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           2       6        2        2        1         4         1
  subtype2           1       3        5        4        9         0         3
  subtype3           0       2        1        3        0         1         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         2         0          0          3          2        2
  subtype2         2         4          1          5          6        1
  subtype3         2         2          2          5          7        2
D4V9, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 13  9
  subtype2 14 17
  subtype3 12 18
  subtype4 17 10
subtype1 subtype2 subtype3 subtype4 
      22       31       30       27 
subtype1 subtype2 subtype3 subtype4 
       9       17       18       10 
$subtype1
TCGA-D3-A2JK TCGA-D3-A3CC TCGA-DA-A1IC TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        6.35        45.70         6.64         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EE-A182 TCGA-EE-A29V TCGA-ER-A19J TCGA-ER-A19N TCGA-FS-A1ZN TCGA-FS-A1ZR 
        1.35         2.43         4.18        42.84        24.00         8.81 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-GN-A261 TCGA-GN-A263 
        6.41         0.20        15.35        15.35 

$subtype2
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
       22.55        10.26        11.41         4.01         2.86        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-EB-A41B TCGA-EB-A42Y TCGA-EE-A17X 
       10.03         9.99         4.93         0.10         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        6.31         4.27        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-ER-A19F TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
        1.08        27.12        11.11        12.10        10.09         5.95 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       53.82        10.78         0.13        31.33        16.21        15.39 
TCGA-GN-A26D 
       14.70 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.47        32.55        70.16        28.08        15.25        13.32 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z4 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
        9.30         5.39         3.88        51.12        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A42Z TCGA-EE-A20B TCGA-EE-A20H 
       25.15         7.00        17.56         0.39        36.07         8.81 
TCGA-EE-A29A TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-ER-A19D 
        7.96         8.12         8.84         6.48         9.67         3.52 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3PL TCGA-FS-A4F2 TCGA-GN-A262 TCGA-GN-A26A 
       12.99        28.64         1.71         3.22        24.85        12.16 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A3CF TCGA-DA-A1HV 
       98.76         8.38        21.14        30.87        24.00        48.79 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 
       39.19        44.52        22.36        14.83         1.12        12.20 
TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        5.13         9.47        12.03         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FW-A3R5 
       25.28        23.90         8.94        78.44        72.16         1.02 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26C 
       84.72        10.09        24.00 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.10     0.39     1.02 
subtype1 subtype2 subtype3 subtype4 
   45.70    53.82    70.16    98.76 
subtype1 subtype2 subtype3 subtype4 
   1.890   10.780   12.575   21.140 
[1] "0.1 - 45.7 (1.9)"  "0.1 - 53.8 (10.8)" "0.4 - 70.2 (12.6)"
[4] "1.0 - 98.8 (21.1)"
  [1] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
  [7] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype1" "subtype3" "subtype3"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [67] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype1"
 [73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [85] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype2" "subtype4" "subtype4" "subtype2" "subtype2" "subtype3"
[109] "subtype4" "subtype2"
  [1] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
  [7] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype1" "subtype3" "subtype3"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [67] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype1"
 [73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [85] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype2" "subtype4" "subtype4" "subtype2" "subtype2" "subtype3"
[109] "subtype4" "subtype2"
  [1] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
  [7] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype3"
 [25] "subtype2" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype1" "subtype3" "subtype3"
 [37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [67] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype1"
 [73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [85] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype2" "subtype4" "subtype4" "subtype2" "subtype2" "subtype3"
[109] "subtype4" "subtype2"
D5V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  6            15
  subtype2                  8             6
  subtype3                  9             2
  subtype4                  4             1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        6
  subtype2                                                                                        6
  subtype3                                                                                       19
  subtype4                                                                                        4
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   5
  subtype2                  36
  subtype3                  30
  subtype4                  41
D5V3, multiclass
D5V4, binary
          cls
clus        0  1
  subtype1 10 22
  subtype2 22 34
  subtype3 27 33
  subtype4 16 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   22
  subtype2   22   34
  subtype3   27   33
  subtype4   16   34
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       22       27       16
  MALE         22       34       33       34
D5V5, binary
          cls
clus        0  1
  subtype1  0 32
  subtype2  1 55
  subtype3  0 60
  subtype4  2 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   32
  subtype2    1   55
  subtype3    0   60
  subtype4    2   48
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        0        2
  YES       32       55       60       48
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 27  2   0   0   1
  subtype2 49  0   1   1   0
  subtype3 51  0   1   1   1
  subtype4 45  0   0   0   1
D5V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 17  1   1   2  0   0   2   2  2  3
  subtype2 32  0   2   6  0   3   4   0  6  0
  subtype3 30  0   3   5  0   1   3   4  6  2
  subtype4 30  1   1   4  1   1   4   0  4  0
D5V7, multiclass
D5V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       1        0        1        3         2         1
  subtype2           2       2        3        5        4         1         6
  subtype3           2       7        1        5        7         2         3
  subtype4           0       7        6        4        6         4         0
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1        11         1          1          3          3        3
  subtype2         8         1          3          6          8        0
  subtype3         2         4          2          5          9        3
  subtype4         1         3          0          6          6        1
D5V9, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 18 20
  subtype2 25 16
  subtype3 13 18
subtype1 subtype2 subtype3 
      38       41       31 
subtype1 subtype2 subtype3 
      20       16       18 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3CC TCGA-DA-A1I4 TCGA-DA-A1IA 
       16.47        10.26         6.35        45.70         9.99         4.93 
TCGA-DA-A1IC TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        6.64         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29E 
       11.57         6.31         1.35         4.27        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29V TCGA-ER-A19J TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-FS-A1ZR 
        1.08         2.43         4.18        12.10        24.00         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
       53.82         3.22        10.78         6.41         0.20         0.13 
TCGA-GN-A264 TCGA-GN-A268 
       31.33        15.39 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CF TCGA-D9-A3Z1 
       98.76        22.55        21.14        11.41        24.00         4.01 
TCGA-D9-A3Z3 TCGA-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 
        2.86         3.88        48.79        35.80        10.03        44.52 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F 
       22.36         7.00        14.83         1.12        12.20         5.13 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       37.97         4.41        27.12         9.47        12.03         9.99 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
       28.64        42.84        78.44        10.09         5.95        72.16 
TCGA-FW-A3R5 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
        1.02        15.35        84.72        16.21        14.70 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3C6 
       32.55        70.16        28.08         8.38        30.87        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       13.32         9.30         5.39        51.12        39.19        13.68 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A42Z TCGA-EE-A20B TCGA-EE-A20H 
       36.69        25.15        17.56         0.39        36.07         8.81 
TCGA-EE-A29A TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-ER-A19D 
        7.96         8.12         8.84         6.48         9.67         3.52 
TCGA-ER-A19L TCGA-ER-A3PL TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A 
       12.99         1.71        15.35        24.85        10.09        12.16 
TCGA-GN-A26C 
       24.00 

subtype1 subtype2 subtype3 
    0.10     1.02     0.39 
subtype1 subtype2 subtype3 
   53.82    98.76    70.16 
subtype1 subtype2 subtype3 
    4.60    14.70    13.32 
[1] "0.1 - 53.8 (4.6)"  "1.0 - 98.8 (14.7)" "0.4 - 70.2 (13.3)"
  [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype2"
  [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype2"
  [1] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype2"
D6V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 14            17
  subtype2                  5             5
  subtype3                  8             2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                       11
  subtype2                                                                                        3
  subtype3                                                                                       21
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  17
  subtype2                  64
  subtype3                  31
D6V3, multiclass
D6V4, binary
          cls
clus        0  1
  subtype1 25 34
  subtype2 25 52
  subtype3 25 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   34
  subtype2   25   52
  subtype3   25   37
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       25       25       25
  MALE         34       52       37
D6V5, binary
          cls
clus        0  1
  subtype1  1 58
  subtype2  1 76
  subtype3  1 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    1   76
  subtype3    1   61
     clus
vv    subtype1 subtype2 subtype3
  NO         1        1        1
  YES       58       76       61
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 53  2   0   0   0
  subtype2 67  0   1   1   2
  subtype3 52  0   1   1   1
D6V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 35  0   1   5  0   0   5   2  5  3
  subtype2 43  1   3   7  1   3   5   0  8  1
  subtype3 31  1   3   5  0   2   3   4  5  1
D6V7, multiclass
D6V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       1        1        2        5         4         6
  subtype2           1       7        8        7        8         4         1
  subtype3           2       9        1        6        7         1         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1        17         0          1          6          9        2
  subtype2         4         4          2         10          8        2
  subtype3         1         5          3          4          9        3
D6V9, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 25 21
  subtype2 14 19
  subtype3 17 13
subtype1 subtype2 subtype3 
      46       33       30 
subtype1 subtype2 subtype3 
      21       19       13 
$subtype1
TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       10.26        30.87        15.25        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB 
       48.79        35.80        39.19        13.68         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XF 
        6.64         7.00         0.43         1.35         1.28         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A17Z TCGA-EE-A181 
        0.53         0.26         0.10         0.39         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27         5.13        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A3PL 
        1.08        27.12         8.84         8.94         4.18         1.71 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       12.10        10.09         5.95        24.00         8.81        53.82 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-IH-A3EA 
       31.33        16.21        15.39        12.59 

$subtype2
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC 
       70.16        98.76         8.38        11.41         6.35        45.70 
TCGA-D3-A3MO TCGA-D9-A3Z4 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.30         3.88        51.12         9.99        44.52        36.69 
TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        0.53         1.18         0.30         8.81         7.96        37.97 
TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.47         9.99         2.43        25.28         9.67         3.52 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A263 
       12.99        28.64         6.58         1.02        15.35        15.35 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26C 
       10.09        12.16        24.00 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE 
       16.47        32.55        28.08        22.55        21.14        13.32 
TCGA-D3-A3MV TCGA-DA-A1I0 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
        5.39        10.03        25.15        19.36        17.56        14.83 
TCGA-EB-A42Y TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A29Q 
        0.20        11.57         1.35        36.07        12.03         8.12 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19N 
        6.48         8.09        11.31        23.90        11.11        42.84 
TCGA-ER-A1A1 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D 
       78.44         0.20         0.13        24.85        84.72        14.70 

subtype1 subtype2 subtype3 
    0.10     0.30     0.13 
subtype1 subtype2 subtype3 
   53.82    98.76    84.72 
subtype1 subtype2 subtype3 
   8.825    9.990   14.765 
[1] "0.1 - 53.8 (8.8)"  "0.3 - 98.8 (10.0)" "0.1 - 84.7 (14.8)"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [73] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[109] "subtype1"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [73] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[109] "subtype1"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [73] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[109] "subtype1"
D7V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 12            16
  subtype2                  9             7
  subtype3                  5             2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                       10
  subtype2                                                                                       17
  subtype3                                                                                        9
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  49
  subtype2                  24
  subtype3                  37
D7V3, multiclass
D7V4, binary
          cls
clus        0  1
  subtype1 32 55
  subtype2 16 41
  subtype3 25 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   55
  subtype2   16   41
  subtype3   25   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       16       25
  MALE         55       41       28
D7V5, binary
          cls
clus        0  1
  subtype1  1 86
  subtype2  1 56
  subtype3  1 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   86
  subtype2    1   56
  subtype3    1   52
     clus
vv    subtype1 subtype2 subtype3
  NO         1        1        1
  YES       86       56       52
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 78  1   1   1   0
  subtype2 52  0   0   0   2
  subtype3 41  1   1   1   1
D7V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 50  1   2   9  0   3   7   2  7  1
  subtype2 32  1   4   4  1   0   5   2  3  2
  subtype3 25  0   2   4  0   2   2   2  7  2
D7V7, multiclass
D7V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       4        5        5       11         4         7
  subtype2           1       8        1        8        3         3         2
  subtype3           2       5        4        2        5         1         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1        13         2          3         10         11        2
  subtype2         6         6          3          3          7        2
  subtype3         3         1          1          8          7        3
D7V9, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 35 31
  subtype2 21 22
subtype1 subtype2 
      66       43 
subtype1 subtype2 
      31       22 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
       16.47        98.76        10.26        30.87         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       45.70        24.00         2.86        48.79        35.80        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        44.52         4.93        22.36         6.64 
TCGA-DA-A3F3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        7.00         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z 
        0.30         0.13         0.53         0.26         0.10         0.39 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D 
        6.31         1.12        12.20         4.27         5.13        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
       38.63         4.41         1.08        27.12         9.47         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19F 
        9.99         2.43         8.09         9.67         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 
        4.18        28.64         6.58         1.71        12.10        10.09 
TCGA-FR-A3YN TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FW-A3TU TCGA-GN-A262 
        5.95        24.00         8.81        53.82         0.13        24.85 
TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-IH-A3EA 
       15.35        31.33        16.21        15.39        14.70        12.59 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        70.16        28.08        22.55         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z4 
       11.41        13.32         9.30         5.39         4.01         3.88 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F5 
       51.12        10.03        36.69        25.15        19.36        17.56 
TCGA-DA-A3F8 TCGA-EB-A42Y TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H 
       14.83         0.20        11.57         1.35        36.07         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A0 
        7.96        37.97        12.03         8.12         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
       25.28        23.90         3.52        12.99        42.84        78.44 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        0.20         1.02        15.35        84.72        10.09        12.16 
TCGA-GN-A26C 
       24.00 

subtype1 subtype2 
     0.1      0.2 
subtype1 subtype2 
   98.76    84.72 
subtype1 subtype2 
    9.57    12.99 
[1] "0.1 - 98.8 (9.6)"  "0.2 - 84.7 (13.0)"
  [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[103] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1"
[1] "hr=" "1.3"
D8V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 17            22
  subtype2                  9             3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                       19
  subtype2                                                                                       17
          vv
clus       REGIONAL LYMPH NODE
  subtype1                  68
  subtype2                  42
D8V3, multiclass
D8V4, binary
          cls
clus        0  1
  subtype1 50 76
  subtype2 23 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   76
  subtype2   23   48
        clus
vv       subtype1 subtype2
  FEMALE       50       23
  MALE         76       48
D8V5, binary
          cls
clus         0   1
  subtype1   1 125
  subtype2   2  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  125
  subtype2    2   69
     clus
vv    subtype1 subtype2
  NO         1        2
  YES      125       69
          vv
clus        M0  M1 M1A M1B M1C
  subtype1 111   1   1   1   2
  subtype2  60   1   1   1   1
D8V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 76  1   5  10  0   3  10   2  8  3
  subtype2 31  1   3   7  1   2   4   4  9  2
D8V7, multiclass
D8V8, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           2       9        8       11       14         5         8
  subtype2           2       8        2        4        5         3         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1        18         3          4         13         13        4
  subtype2         4         6          3          8         12        3
D8V9, multiclass
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
               "PRIMARY.SITE.OF.DISEASE" 
                                      V4 
                                "GENDER" 
                                      V5 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V6 
                    "DISTANT.METASTASIS" 
                                      V7 
                 "LYMPH.NODE.METASTASIS" 
                                      V8 
                       "TUMOR.STAGECODE" 
                                      V9 
                 "NEOPLASM.DISEASESTAGE" 
> q(save="no")
