
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/3215668/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         3004           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 
        1390           NA           NA           NA          164           NA 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
          NA           NA           NA          122           87         1484 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA         1555           NA         1192           NA           NA 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        1116           NA          680           NA          589           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A17Z 
         534          451            6            6           NA           NA 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
          NA           NA           NA         1097          156         1155 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
          NA         1175          134           NA           NA          366 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
         247          269          304          197           NA           NA 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
         769          727           NA          272           NA           NA 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
          NA           NA           NA           NA           NA           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           NA           NA           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
          NA         1303           NA         2386          200           52 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
         181         2195           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           NA           NA 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 
          NA           NA           NA         1637           NA          328 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A261 
          NA          195           69           31           NA           NA 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
         756           NA         2577           NA           NA           NA 
TCGA-GN-A26A TCGA-GN-A26D 
          NA          447 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=42,	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  6  8
  subtype2  7  9
  subtype3  9 14
  subtype4 17 13
subtype1 subtype2 subtype3 subtype4 
      14       16       23       30 
subtype1 subtype2 subtype3 subtype4 
       8        9       14       13 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A3MO TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A185 
       16.47         9.30        39.19         7.00         6.31         4.27 
TCGA-EE-A20B TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-ER-A19D TCGA-ER-A3ET 
       36.07         1.08         8.84         9.99         3.52         6.58 
TCGA-FR-A3YN TCGA-GN-A267 
        5.95        16.21 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D9-A3Z3 TCGA-DA-A1HW 
       32.55        22.55        45.70         5.39         2.86        35.80 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A6 
       36.69        25.15        17.56         6.48         8.09         8.94 
TCGA-ER-A19L TCGA-ER-A19M TCGA-GN-A264 TCGA-GN-A26A 
       12.99        28.64        31.33        12.16 

$subtype3
TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1HY 
       70.16        10.26        15.25        13.32        48.79        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29D 
       13.68         9.99         6.64         1.12         5.13        11.15 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-ER-A19F TCGA-ER-A19J 
        4.41        12.03         8.12         9.67        11.11         4.18 
TCGA-ER-A19N TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-GN-A268 TCGA-GN-A26D 
       42.84         1.71         8.81        15.39        14.70 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       98.76        28.08         8.38        21.14        11.41         6.35 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       24.00         4.01        10.03        22.36        19.36        14.83 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A2A0 
       11.57        12.20        37.97        38.63         9.47        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 
       25.28        23.90        78.44        72.16        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02        15.35        24.85        84.72        10.09 

subtype1 subtype2 subtype3 subtype4 
    1.08     2.86     1.12     1.02 
subtype1 subtype2 subtype3 subtype4 
   39.19    45.70    70.16    98.76 
subtype1 subtype2 subtype3 subtype4 
   7.920   20.055   11.110   17.355 
[1] "1.1 - 39.2 (7.9)"  "2.9 - 45.7 (20.1)" "1.1 - 70.2 (11.1)"
[4] "1.0 - 98.8 (17.4)"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype4"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype4" "subtype1"
[25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype3"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype4"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype4"
[55] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype1"
[67] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
[73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[79] "subtype4" "subtype1" "subtype3" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype4"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype4" "subtype1"
[25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype3"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype4"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype4"
[55] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype1"
[67] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
[73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[79] "subtype4" "subtype1" "subtype3" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[13] "subtype2" "subtype3" "subtype4" "subtype1" "subtype2" "subtype4"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype4" "subtype1"
[25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype3"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype4"
[43] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[49] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype4"
[55] "subtype4" "subtype4" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype1"
[67] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
[73] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype4"
[79] "subtype4" "subtype1" "subtype3" "subtype2" "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 11 15
  subtype2 17 16
  subtype3 14 15
subtype1 subtype2 subtype3 
      26       33       29 
subtype1 subtype2 subtype3 
      15       16       15 
$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-D3-A3MV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EE-A17Z 
        5.39        13.68        36.69         7.00         0.20         6.31 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L 
       36.07        11.15         8.84         9.67         3.52        12.99 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3R5 
        6.58         1.71         8.81         5.98         2.27         1.02 
TCGA-GN-A267 TCGA-GN-A26D 
       16.21        14.70 

$subtype2
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-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F 
       22.36        19.36        17.56        14.83        12.20         5.13 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
       37.97        38.63         9.47         6.48        11.31        25.28 
TCGA-EE-A2A6 TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-GN-A261 
        8.94        28.64        42.84        78.44        72.16        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       84.72        10.09        12.16 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.55         6.35        15.25        48.79        51.12        39.19 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 
       25.15         6.64         0.20        11.57         1.12         4.27 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
        4.41         1.08        12.03         8.12         9.99         8.09 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-FR-A3YN TCGA-FS-A4F0 TCGA-FS-A4F5 
       23.90        11.11         4.18         5.95        53.82        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       10.78         6.41        24.85        31.33        15.39 

subtype1 subtype2 subtype3 
    0.20     2.86     0.20 
subtype1 subtype2 subtype3 
   45.70    98.76    53.82 
subtype1 subtype2 subtype3 
   9.485   17.560   11.110 
[1] "0.2 - 45.7 (9.5)"  "2.9 - 98.8 (17.6)" "0.2 - 53.8 (11.1)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[85] "subtype1" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[85] "subtype1" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[85] "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  8  9
  subtype2  6  8
  subtype3  5 13
subtype1 subtype2 subtype3 
      17       14       18 
subtype1 subtype2 subtype3 
       9        8       13 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I8 
       16.47        70.16         8.38        51.12         9.99        25.15 
TCGA-DA-A1IB TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29T 
       22.36         5.13        37.97        38.63         8.84         6.48 
TCGA-EE-A2A0 TCGA-ER-A19D TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       11.31         3.52        84.72        16.21        12.16 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-EE-A29P 
       32.55        98.76        28.08        13.32        48.79        12.03 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-GN-A264 
       23.90        11.11         4.18        12.99        42.84        31.33 
TCGA-GN-A266 TCGA-GN-A26D 
       10.09        14.70 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IC 
       22.55        10.26        11.41        35.80        13.68         6.64 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       11.57         1.12         4.27         4.41         1.08         9.47 
TCGA-EE-A29S TCGA-EE-A2A6 TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A268 
        9.99         8.94        78.44        15.35        24.85        15.39 

subtype1 subtype2 subtype3 
    3.52     4.18     1.08 
subtype1 subtype2 subtype3 
   84.72    98.76    78.44 
subtype1 subtype2 subtype3 
  16.210   19.300   10.835 
[1] "3.5 - 84.7 (16.2)" "4.2 - 98.8 (19.3)" "1.1 - 78.4 (10.8)"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "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  5  7
  subtype2  4  7
  subtype3  3 12
  subtype4  7  4
subtype1 subtype2 subtype3 subtype4 
      12       11       15       11 
subtype1 subtype2 subtype3 subtype4 
       7        7       12        4 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-EE-A29C 
       16.47        70.16         8.38        51.12         9.99        37.97 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2A0 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       38.63         8.84        11.31        84.72        16.21        12.16 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-DA-A1I8 TCGA-EE-A29S TCGA-EE-A2A2 TCGA-ER-A19D 
       32.55        28.08        25.15         9.99        23.90         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-GN-A266 TCGA-GN-A26D 
       11.11         4.18        42.84        10.09        14.70 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-EE-A17X 
       10.26        11.41        13.32        13.68         6.64        11.57 
TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 
        4.27         4.41         1.08        12.99        78.44        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       24.85        31.33        15.39 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1IB TCGA-EE-A181 
       98.76        22.55        48.79        35.80        22.36         1.12 
TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        5.13         9.47        12.03         6.48         8.94 

subtype1 subtype2 subtype3 subtype4 
    8.38     3.52     1.08     1.12 
subtype1 subtype2 subtype3 subtype4 
   84.72    42.84    78.44    98.76 
subtype1 subtype2 subtype3 subtype4 
   16.34    14.70    12.99    12.03 
[1] "8.4 - 84.7 (16.3)" "3.5 - 42.8 (14.7)" "1.1 - 78.4 (13.0)"
[4] "1.1 - 98.8 (12.0)"
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype4" "subtype4"
[13] "subtype1" "subtype3" "subtype1" "subtype2" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype4" "subtype4" "subtype1" "subtype2"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype4" "subtype4"
[13] "subtype1" "subtype3" "subtype1" "subtype2" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype4" "subtype4" "subtype1" "subtype2"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype4"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype4" "subtype4"
[13] "subtype1" "subtype3" "subtype1" "subtype2" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[25] "subtype3" "subtype3" "subtype4" "subtype4" "subtype1" "subtype2"
[31] "subtype4" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[49] "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 11 19
  subtype2 14  7
  subtype3 12 18
subtype1 subtype2 subtype3 
      30       21       30 
subtype1 subtype2 subtype3 
      19        7       18 
$subtype1
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-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 
        9.30         5.39        51.12        39.19        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29Q TCGA-EE-A29R 
       25.15         7.00        17.56        36.07         8.12         8.84 
TCGA-EE-A29T TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        6.48         9.67         3.52         4.18        12.99        28.64 
TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A 
        1.71         8.81        15.35        24.85        10.09        12.16 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1IB 
       98.76         8.38        21.14        24.00        48.79        22.36 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P 
       14.83         1.12        12.20         5.13         9.47        12.03 
TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19N 
        9.99        11.31        25.28        23.90         8.94        42.84 
TCGA-ER-A1A1 TCGA-FR-A44A TCGA-GN-A265 
       78.44        72.16        84.72 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D9-A3Z1 
       22.55        10.26        11.41         6.35        45.70         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A17X 
        2.86        35.80        10.03         9.99         6.64        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-A29X TCGA-ER-A19F TCGA-FR-A3YN TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.08         8.09        11.11         5.95        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        6.41         1.02        31.33        16.21        15.39        14.70 

subtype1 subtype2 subtype3 
    1.71     1.12     1.02 
subtype1 subtype2 subtype3 
   70.16    98.76    53.82 
subtype1 subtype2 subtype3 
   13.50    21.14    10.52 
[1] "1.7 - 70.2 (13.5)" "1.1 - 98.8 (21.1)" "1.0 - 53.8 (10.5)"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[79] "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" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[79] "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" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[79] "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  9 16
  subtype2 21 14
  subtype3  7 14
subtype1 subtype2 subtype3 
      25       35       21 
subtype1 subtype2 subtype3 
      16       14       14 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3C6 
       16.47        32.55        70.16        28.08         8.38        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
       13.32         9.30         5.39        51.12        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A5 
       25.15        17.56        36.07         8.84        11.31         9.67 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        3.52        12.99         1.71        24.85        84.72        10.09 
TCGA-GN-A26A 
       12.16 

$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-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1IB 
        2.86        48.79        35.80        10.03        39.19        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29H 
        7.00        14.83         1.12        12.20         5.13         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.12         9.99         6.48         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A19N 
       25.28        23.90         8.94        11.11        28.64        42.84 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FW-A3R5 TCGA-GN-A267 
       78.44         5.95        72.16         1.02        16.21 

$subtype3
TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3CC TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A17X 
       10.26         6.35        45.70         9.99         6.64        11.57 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        6.31         4.27        37.97        11.15        38.63         1.08 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-GN-A261 
        4.18         8.81        53.82        10.78         6.41        15.35 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        15.39        14.70 

subtype1 subtype2 subtype3 
    1.71     1.02     1.08 
subtype1 subtype2 subtype3 
   84.72    98.76    53.82 
subtype1 subtype2 subtype3 
   13.68    12.03    10.78 
[1] "1.7 - 84.7 (13.7)" "1.0 - 98.8 (12.0)" "1.1 - 53.8 (10.8)"
 [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" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[79] "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" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[79] "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" "subtype1" "subtype2" "subtype2"
[25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[67] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[79] "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 11 16
  subtype2  9  8
  subtype3 16 20
subtype1 subtype2 subtype3 
      27       17       36 
subtype1 subtype2 subtype3 
      16        8       20 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.47        10.26        24.00         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EE-A17Z 
       35.80        13.68        22.36         6.64         7.00         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E 
        1.12        12.20         4.27         5.13        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29X TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-FR-A3YN 
        4.41         1.08         8.09         8.94         1.71         5.95 
TCGA-FS-A4F0 TCGA-GN-A267 TCGA-GN-A268 
       53.82        16.21        15.39 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I0 
       32.55        28.08        22.55        13.32         5.39        10.03 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 
       25.15        17.56        14.83        36.07        12.03        11.31 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D 
       23.90        11.11        24.85        84.72        14.70 

$subtype3
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76         8.38        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       15.25        45.70         9.30        51.12        39.19         9.99 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29N TCGA-EE-A29Q 
       36.69        19.36        11.57        37.97         9.47         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        8.84         9.99         6.48        25.28         9.67         3.52 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-FS-A1ZR TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
        8.81         1.02        15.35        31.33        10.09        12.16 

subtype1 subtype2 subtype3 
    1.08     5.39     1.02 
subtype1 subtype2 subtype3 
   53.82    84.72    98.76 
subtype1 subtype2 subtype3 
   8.940   17.560   11.865 
[1] "1.1 - 53.8 (8.9)"  "5.4 - 84.7 (17.6)" "1.0 - 98.8 (11.9)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[79] "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" "subtype1" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[79] "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" "subtype1" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[79] "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  7 11
  subtype2  7  4
  subtype3 22 29
subtype1 subtype2 subtype3 
      18       11       51 
subtype1 subtype2 subtype3 
      11        4       29 
$subtype1
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1HY 
       70.16         8.38        21.14        11.41        13.32        51.12 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A29Q TCGA-EE-A29T 
       36.69        25.15        17.56        11.57         8.12         6.48 
TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A266 TCGA-GN-A26A 
        3.52        42.84        78.44        15.35        10.09        12.16 

$subtype2
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A3MV TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F8 
       28.08        22.55         5.39        10.03        19.36        14.83 
TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-GN-A265 
       36.07        12.03        11.31        23.90        84.72 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 
       16.47        32.55        98.76        10.26         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       45.70        24.00         9.30         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.80        39.19        13.68         9.99        22.36         6.64 
TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
        7.00         6.31         1.12        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.84         9.99         8.09        25.28         9.67         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL 
       11.11         4.18        12.99        28.64         6.58         1.71 
TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 
        5.95         8.81        53.82         1.02        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

subtype1 subtype2 subtype3 
    3.52     5.39     1.02 
subtype1 subtype2 subtype3 
   78.44    84.72    98.76 
subtype1 subtype2 subtype3 
  14.335   19.360   10.260 
[1] "3.5 - 78.4 (14.3)" "5.4 - 84.7 (19.4)" "1.0 - 98.8 (10.3)"
 [1] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[79] "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" "subtype3" "subtype1" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[79] "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" "subtype3" "subtype1" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[79] "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")
