
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_LN/3157616/1.GDAC_mergedClustering.Finished/SKCM-Regional_LN.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_LN/3215665/SKCM-Regional_LN.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=116, in cluster file=116, common to both=116
[1]   8 116
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
30 18 38 26 
 1  2  3  4 
30 18 38 26 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
20 40 27 29 
 1  2  3  4 
20 40 27 29 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
12 24 15 14 15 
 1  2  3  4  5 
12 24 15 14 15 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
12 22 34 12 
 1  2  3  4 
12 22 34 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
42 27 43 
 1  2  3 
42 27 43 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
18 29 34 31 
 1  2  3  4 
18 29 34 31 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
42 23 45 
 1  2  3 
42 23 45 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
11 25 74 
 1  2  3 
11 25 74 
[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 116 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
          NA           NA         3687           NA           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
          NA         4511           82          194          345           98 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
        1487           NA         3564           NA          713           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A17Z 
        6553          477           28          309           NA           NA 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
          NA           NA           NA         2399         1455           NA 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        1205          979           NA           NA         1716          440 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        1700        10523           NA           NA         2401          743 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        1787         1446         1315         4134         5536          686 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
        2717         1664         1673         1691          595         2042 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
          NA         3931           NA           NA           NA           NA 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
          NA           NA           NA           NA           NA         4403 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
        6175           NA           NA         7562           NA         3150 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        4150         1265          129         3733          786          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
         813           NA           NA           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
          NA         1340           NA         2433         2448         4885 
TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F9 TCGA-FS-A4FB 
          NA           NA         4525         1505          378           NA 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2369          699           NA           NA         2577           NA 
TCGA-GN-A268 TCGA-GN-A26D 
          NA         1204 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=61,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=24,	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=4,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  4   4  10   3  14  12   4   3  13   7   1   5  15   1  10 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 116 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=4, 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 16 14
  subtype2  7 11
  subtype3 19 19
  subtype4 13 11
subtype1 subtype2 subtype3 subtype4 
      30       18       38       24 
subtype1 subtype2 subtype3 subtype4 
      14       11       19       11 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.57        43.40        58.03         6.38         3.22        48.89 
TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29P 
       10.49         8.65         4.93        13.97         2.56        56.42 
TCGA-EE-A29S TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MD 
       55.89        47.54        89.33        55.59        67.13        47.28 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD 
      204.62       203.01        47.54       136.44       122.73         3.68 
TCGA-ER-A19F TCGA-ER-A19N TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-GN-A268 TCGA-GN-A26D 
       26.37        44.05        80.48        32.71        62.76        39.58 

$subtype2
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A181 
      112.54        36.03       117.17       176.55       215.44        33.73 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2M6 TCGA-EE-A3AE TCGA-EE-A3AH 
       47.84        39.62       345.96       129.24        26.73       138.77 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-GN-A264 TCGA-GN-A267 
      131.08        61.05         7.76        53.52       117.93        64.41 

$subtype3
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      121.22        28.08        65.49        23.77        11.87        12.10 
TCGA-D9-A3Z1 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A29N 
       11.34        23.44        15.68        29.82        26.86        18.58 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       17.92        46.82        24.43        43.23       135.91       182.01 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MC 
       22.55        54.71        55.00        19.56        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR 
      103.27       103.17        96.23       167.87        43.23       103.56 
TCGA-EE-A3AA TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZP TCGA-FS-A1ZW 
        4.24        79.99       160.60        28.08        74.73        49.48 
TCGA-FS-A4F9 TCGA-GN-A265 
       12.43        84.72 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A1JW TCGA-EE-A20F 
       31.59        60.23        24.53       148.31         2.70        78.87 
TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2M5 TCGA-EE-A2M7 
       32.19        14.47        78.94        58.75        21.67        28.80 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
       16.96       144.76       248.61        41.59        25.84        13.81 
TCGA-ER-A19J TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FW-A3R5 
        6.41       216.92         9.70        47.38       148.77        22.98 

subtype1 subtype2 subtype3 subtype4 
    2.56     7.76     4.24     2.70 
subtype1 subtype2 subtype3 subtype4 
  204.62   345.96   182.01   248.61 
subtype1 subtype2 subtype3 subtype4 
  47.410   88.475   43.230   31.890 
[1] "2.6 - 204.6 (47.4)" "7.8 - 346.0 (88.5)" "4.2 - 182.0 (43.2)"
[4] "2.7 - 248.6 (31.9)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [13] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype1"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype1" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [37] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype4" "subtype1" "subtype3" "subtype4" "subtype1" "subtype3"
 [73] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype1" "subtype2" "subtype4"
 [85] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
 [97] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [13] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype1"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype1" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [37] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype4" "subtype1" "subtype3" "subtype4" "subtype1" "subtype3"
 [73] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype1" "subtype2" "subtype4"
 [85] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
 [97] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [13] "subtype4" "subtype4" "subtype4" "subtype1" "subtype3" "subtype1"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype1" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [37] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
 [61] "subtype4" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype4" "subtype1" "subtype3" "subtype4" "subtype1" "subtype3"
 [73] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype1" "subtype2" "subtype4"
 [85] "subtype2" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype2"
 [97] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype1"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 11 19
  subtype2  4 14
  subtype3 10 28
  subtype4 10 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   19
  subtype2    4   14
  subtype3   10   28
  subtype4   10   16
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       11        4       10       10
  MALE         19       14       28       16
          vv
clus       M0 M1 M1B M1C
  subtype1 25  0   0   1
  subtype2 16  0   0   0
  subtype3 35  0   1   0
  subtype4 22  1   1   0
D1V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 17  0   1   2  0   0   2   1  3  1
  subtype2  8  0   1   3  0   0   1   0  2  1
  subtype3 23  1   1   2  0   1   3   0  5  0
  subtype4 13  0   0   3  1   2   2   0  3  0
D1V5, multiclass
D1V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       1        2        3        3         1         4
  subtype2           1       1        1        2        2         1         0
  subtype3           0      10        2        3        3         3         1
  subtype4           0       3        2        3        5         0         0
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         2         0          1          3          4        1
  subtype2         0         0          1          2          4        0
  subtype3         0         1          1          3          7        1
  subtype4         0         3          0          2          3        1
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  9
  subtype2 19 19
  subtype3 11 16
  subtype4 17 12
subtype1 subtype2 subtype3 subtype4 
      20       38       27       29 
subtype1 subtype2 subtype3 subtype4 
       9       19       16       12 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EE-A29C 
       16.57       112.54        43.40       215.44        10.16        47.84 
TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       39.62       345.96       204.62       136.44        41.59        25.84 
TCGA-ER-A19L TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4FD 
      131.08         7.76        53.52        47.38       148.77        77.88 
TCGA-GN-A267 TCGA-GN-A26D 
       64.41        39.58 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CF 
      121.22        28.08        65.49        23.77        11.87        24.53 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A183 
       11.34         3.22        36.03        23.44        15.68        26.86 
TCGA-EE-A29N TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
       18.58        46.82        78.94        58.75       135.91       182.01 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       54.71        55.00        19.56        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA 
      103.27       103.17        16.96        96.23       103.56         4.24 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A1Z4 TCGA-FS-A1ZH 
       61.05        44.05        79.99       160.60        28.08        32.71 
TCGA-FS-A1ZW TCGA-GN-A265 
       49.48        84.72 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1HV 
       31.59        12.10        58.03        60.23         6.38        48.89 
TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29R 
      176.55        10.49         8.65        33.73        78.87        14.47 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MK 
       47.54        22.55        55.59       129.24        28.80       144.76 
TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-FS-A1YW 
      248.61        26.73       138.77        26.37         6.41       216.92 
TCGA-FS-A1ZP TCGA-FS-A4FB TCGA-GN-A264 
       74.73        26.73       117.93 

$subtype4
TCGA-D9-A148 TCGA-D9-A1JW TCGA-DA-A1HY TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A185 
      148.31         2.70       117.17         0.92        29.82         4.93 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X 
       13.97        32.19         2.56        56.42        55.89        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2ML 
       24.43        43.23        89.33        67.13        47.28       203.01 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
      167.87        47.54        43.23       122.73         3.68        13.81 
TCGA-FR-A3YN TCGA-FS-A1ZG TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A268 
       80.48         9.70        12.43        22.98        62.76 

subtype1 subtype2 subtype3 subtype4 
    7.76     3.22     6.38     0.92 
subtype1 subtype2 subtype3 subtype4 
  345.96   182.01   248.61   203.01 
subtype1 subtype2 subtype3 subtype4 
  50.680   45.435   47.540   43.230 
[1] "7.8 - 346.0 (50.7)" "3.2 - 182.0 (45.4)" "6.4 - 248.6 (47.5)"
[4] "0.9 - 203.0 (43.2)"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
 [37] "subtype1" "subtype4" "subtype4" "subtype2" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [49] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
 [55] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [73] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype2"
 [79] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype4" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[103] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype1"
[109] "subtype4" "subtype3" "subtype2" "subtype1" "subtype4" "subtype1"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
 [37] "subtype1" "subtype4" "subtype4" "subtype2" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [49] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
 [55] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [73] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype2"
 [79] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype4" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[103] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype1"
[109] "subtype4" "subtype3" "subtype2" "subtype1" "subtype4" "subtype1"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
 [37] "subtype1" "subtype4" "subtype4" "subtype2" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [49] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
 [55] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [73] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype2"
 [79] "subtype1" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype4" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[103] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype1"
[109] "subtype4" "subtype3" "subtype2" "subtype1" "subtype4" "subtype1"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  4 16
  subtype2 11 29
  subtype3 11 16
  subtype4 11 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   16
  subtype2   11   29
  subtype3   11   16
  subtype4   11   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       11       11       11
  MALE         16       29       16       18
          vv
clus       M0 M1 M1B M1C
  subtype1 17  0   0   0
  subtype2 35  0   1   1
  subtype3 25  1   0   0
  subtype4 25  0   1   0
D2V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 10  0   1   2  0   0   1   0  3  1
  subtype2 22  1   1   4  0   0   3   1  5  0
  subtype3 15  0   2   2  0   1   4   0  1  1
  subtype4 14  0   0   2  1   2   1   0  6  0
D2V5, multiclass
D2V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       1        0        2        2         1         2
  subtype2           0      10        1        4        3         3         0
  subtype3           0       2        2        3        6         0         1
  subtype4           0       2        4        2        2         1         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          1          2          4        0
  subtype2         0         2          0          5          6        2
  subtype3         0         2          1          3          3        1
  subtype4         1         1          1          1          7        0
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  6  6
  subtype2 10 14
  subtype3 11  4
  subtype4  4 10
  subtype5 10  4
subtype1 subtype2 subtype3 subtype4 subtype5 
      12       24       15       14       14 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       14        4       10        4 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       16.57        65.49       117.17        78.87        47.84        39.62 
TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-GN-A265 TCGA-GN-A267 
       14.47        46.82        21.67        61.51        84.72        64.41 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A3CE TCGA-EE-A29S TCGA-EE-A2GL TCGA-EE-A2MI 
      112.54        28.08        60.23        55.89        55.00       204.62 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
      144.76       203.01       167.87        47.54       248.61       136.44 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
      122.73        25.84        26.73        26.37         6.41       131.08 
TCGA-ER-A19N TCGA-FS-A1YW TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       44.05       216.92        53.52        32.71        47.38        74.73 

$subtype3
TCGA-D3-A1Q7 TCGA-DA-A1HV TCGA-DA-A1IB TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29P 
      121.22        48.89        23.44        33.73        18.58        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 
      345.96        58.75        54.71        19.56        67.13        19.76 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA 
       96.23       103.56         4.24 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A2A2 
       31.59        43.40        11.87        29.82         2.56        24.43 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A3AF TCGA-ER-A1A1 TCGA-FS-A1Z4 TCGA-GN-A264 
      129.24        47.28        13.81        79.99        28.08       117.93 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

$subtype5
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A185 
      148.31         2.70         6.38        36.03       176.55         4.93 
TCGA-EE-A29H TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MT 
       32.19        43.23       182.01        22.55        55.59        41.59 
TCGA-EE-A3AD TCGA-FS-A1ZG 
        3.68         9.70 

subtype1 subtype2 subtype3 subtype4 subtype5 
   14.47     6.41     4.24     2.56     2.70 
subtype1 subtype2 subtype3 subtype4 subtype5 
  117.17   248.61   345.96   129.24   182.01 
subtype1 subtype2 subtype3 subtype4 subtype5 
  54.675   58.060   54.710   35.585   34.110 
[1] "14.5 - 117.2 (54.7)" "6.4 - 248.6 (58.1)"  "4.2 - 346.0 (54.7)" 
[4] "2.6 - 129.2 (35.6)"  "2.7 - 182.0 (34.1)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype1" "subtype4" "subtype2" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype5" "subtype1" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype1" "subtype1" "subtype1" "subtype5"
[25] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype4" "subtype3" "subtype5" "subtype5" "subtype5"
[37] "subtype3" "subtype2" "subtype5" "subtype3" "subtype3" "subtype1"
[43] "subtype4" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype5" "subtype3" "subtype2" "subtype2" "subtype5"
[61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype4" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
[73] "subtype2" "subtype2" "subtype4" "subtype1" "subtype1" "subtype4"
[79] "subtype4"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype1" "subtype4" "subtype2" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype5" "subtype1" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype1" "subtype1" "subtype1" "subtype5"
[25] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype4" "subtype3" "subtype5" "subtype5" "subtype5"
[37] "subtype3" "subtype2" "subtype5" "subtype3" "subtype3" "subtype1"
[43] "subtype4" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype5" "subtype3" "subtype2" "subtype2" "subtype5"
[61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype4" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
[73] "subtype2" "subtype2" "subtype4" "subtype1" "subtype1" "subtype4"
[79] "subtype4"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype4" "subtype4"
 [7] "subtype1" "subtype4" "subtype2" "subtype5" "subtype5" "subtype5"
[13] "subtype3" "subtype5" "subtype1" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype1" "subtype1" "subtype1" "subtype5"
[25] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype4" "subtype3" "subtype5" "subtype5" "subtype5"
[37] "subtype3" "subtype2" "subtype5" "subtype3" "subtype3" "subtype1"
[43] "subtype4" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype5" "subtype3" "subtype2" "subtype2" "subtype5"
[61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype4" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
[73] "subtype2" "subtype2" "subtype4" "subtype1" "subtype1" "subtype4"
[79] "subtype4"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  3  9
  subtype2  8 16
  subtype3  9  6
  subtype4  3 11
  subtype5  6  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    9
  subtype2    8   16
  subtype3    9    6
  subtype4    3   11
  subtype5    6    9
          vv
clus       M0 M1 M1B M1C
  subtype1 11  0   0   0
  subtype2 17  1   1   1
  subtype3 14  0   0   0
  subtype4 11  0   0   0
  subtype5 13  0   1   0
D3V4, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1  6  0   1   2   0   0   0  2  0
  subtype2 16  0   0   1   0   0   1  2  0
  subtype3 10  1   0   0   0   2   0  0  1
  subtype4  7  0   0   2   1   0   0  2  0
  subtype5  6  0   0   2   1   2   0  2  1
D3V5, multiclass
D3V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       2        0        2        1         1         0
  subtype2           1       4        1        1        4         3         1
  subtype3           0       2        2        1        2         1         0
  subtype4           0       2        1        0        1         0         2
  subtype5           0       1        2        2        0         0         1
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         0          1          1          3        0
  subtype2         0         1          0          0          0        3
  subtype3         1         1          0          1          1        0
  subtype4         1         0          0          2          3        0
  subtype5         0         0          0          2          3        0
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 10  2
  subtype2 11 11
  subtype3 15 19
  subtype4  5  6
subtype1 subtype2 subtype3 subtype4 
      12       22       34       11 
subtype1 subtype2 subtype3 subtype4 
       2       11       19        6 
$subtype1
TCGA-D3-A1Q7 TCGA-DA-A1HV TCGA-DA-A1IB TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P 
      121.22        48.89        23.44        78.87        18.58        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GU TCGA-EE-A2M8 
      345.96        58.75       182.01        54.71        67.13        19.76 

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

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A148 TCGA-D9-A1JW 
       31.59        43.40        11.87        60.23       148.31         2.70 
TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 
        6.38        36.03       176.55        29.82        33.73         4.93 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MD 
       32.19         2.56        43.23        22.55        55.59        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       96.23       144.76       203.01       248.61       136.44        41.59 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FS-A1YW TCGA-FS-A1ZG 
        3.68        26.73       131.08        79.99       216.92         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-GN-A264 TCGA-GN-A268 
       47.38        74.73       117.93        62.76 

$subtype4
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-DA-A1HY TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29R 
       16.57        65.49       117.17        47.84        39.62        14.47 
TCGA-EE-A2A0 TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-GN-A265 TCGA-GN-A267 
       46.82        21.67        61.51        84.72        64.41 

subtype1 subtype2 subtype3 subtype4 
   18.58     4.24     2.56    14.47 
subtype1 subtype2 subtype3 subtype4 
  345.96   204.62   248.61   117.17 
subtype1 subtype2 subtype3 subtype4 
  57.585   41.815   45.340   47.840 
[1] "18.6 - 346.0 (57.6)" "4.2 - 204.6 (41.8)"  "2.6 - 248.6 (45.3)" 
[4] "14.5 - 117.2 (47.8)"
 [1] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[79] "subtype2"
 [1] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[79] "subtype2"
 [1] "subtype4" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [7] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype4" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype1"
[31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype4"
[43] "subtype2" "subtype1" "subtype4" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[79] "subtype2"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  8  4
  subtype2  5 17
  subtype3 13 21
  subtype4  3  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    4
  subtype2    5   17
  subtype3   13   21
  subtype4    3    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8        5       13        3
  MALE          4       17       21        9
          vv
clus       M0 M1 M1B M1C
  subtype1 12  0   0   0
  subtype2 13  1   1   1
  subtype3 30  0   1   0
  subtype4 11  0   0   0
D4V4, multiclass
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1  8  1   0   0   0   2   0  0  1
  subtype2 13  0   0   1   0   0   1  2  0
  subtype3 19  0   0   3   2   2   0  4  1
  subtype4  5  0   1   3   0   0   0  2  0
D4V5, multiclass
D4V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       2        2        1        1         0         0
  subtype2           1       5        0        0        0         4         1
  subtype3           0       2        4        3        7         0         3
  subtype4           0       2        0        2        0         1         0
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         1          0          1          1        0
  subtype2         1         0          0          1          0        3
  subtype3         0         1          0          2          6        0
  subtype4         0         0          1          2          3        0
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 20 22
  subtype2 14 12
  subtype3 21 21
subtype1 subtype2 subtype3 
      42       26       42 
subtype1 subtype2 subtype3 
      22       12       21 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX 
       16.57       112.54        28.08        58.03        60.23         6.38 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29P 
      117.17       176.55        10.49       215.44        78.87        56.42 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GE 
       14.47        55.89       345.96        46.82        43.23       135.91 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        22.55        55.59        21.67       129.24        28.80 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       61.51       204.62       144.76       167.87       248.61       136.44 
TCGA-EE-A3AB TCGA-EE-A3AH TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-FS-A1YW 
      122.73       138.77         6.41       131.08        61.05       216.92 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW 
        7.76        53.52        32.71        74.73       148.77        49.48 

$subtype2
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1IB 
      121.22        65.49        23.77        24.53        48.89        23.44 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29N TCGA-EE-A2A1 TCGA-EE-A2A2 
       15.68        33.73        26.86        18.58        78.94        24.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       54.71        55.00        19.56        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-ER-A19N TCGA-ER-A1A1 
       16.96        96.23       103.56         4.24        44.05        79.99 
TCGA-FS-A1Z4 TCGA-GN-A265 
       28.08        84.72 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D9-A148 TCGA-D9-A1JW 
       31.59        43.40        11.87        12.10       148.31         2.70 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A185 
       11.34         3.22        36.03        29.82         8.65         4.93 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29X 
       47.84        13.97        39.62        32.19         2.56        17.92 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2ML 
       58.75        47.54        89.33        67.13        47.28       203.01 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       47.54        43.23        41.59        25.84         3.68        26.73 
TCGA-EE-A3AF TCGA-ER-A19F TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       13.81        26.37        80.48       160.60         9.70        47.38 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       12.43        22.98       117.93        64.41        62.76        39.58 

subtype1 subtype2 subtype3 
    6.38     4.24     2.56 
subtype1 subtype2 subtype3 
  345.96   121.22   203.01 
subtype1 subtype2 subtype3 
   61.28    38.89    34.11 
[1] "6.4 - 346.0 (61.3)" "4.2 - 121.2 (38.9)" "2.6 - 203.0 (34.1)"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [97] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [97] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [31] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [73] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [97] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 13 29
  subtype2  8 19
  subtype3 14 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   29
  subtype2    8   19
  subtype3   14   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13        8       14
  MALE         29       19       29
          vv
clus       M0 M1 M1B M1C
  subtype1 37  1   1   1
  subtype2 24  0   0   0
  subtype3 37  0   1   0
D5V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 26  0   1   3  0   0   2   1  5  2
  subtype2 15  1   0   2  0   0   3   0  3  0
  subtype3 20  0   2   5  1   3   3   0  5  0
D5V5, multiclass
D5V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           1       7        1        4        7         3         2
  subtype2           0       6        0        3        3         2         0
  subtype3           0       2        6        4        3         0         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         1          0          2          6        3
  subtype2         0         1          0          4          4        0
  subtype3         1         2          3          4          8        0
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 11  6
  subtype2 15 13
  subtype3 14 20
  subtype4 15 16
subtype1 subtype2 subtype3 subtype4 
      17       28       34       31 
subtype1 subtype2 subtype3 subtype4 
       6       13       20       16 
$subtype1
TCGA-D3-A1Q9 TCGA-D9-A148 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A3F3 TCGA-EE-A20F 
       31.59       148.31         3.22        36.03        10.49        78.87 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2MD TCGA-EE-A3AE 
       47.54        43.23       182.01        22.55        47.28        26.73 
TCGA-ER-A19F TCGA-ER-A19M TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZW 
       26.37        61.05        80.48       160.60        49.48 

$subtype2
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1IB TCGA-DA-A3F8 
       23.77        11.87        24.53        48.89        23.44        15.68 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A1 
       33.73        26.86        18.58        56.42        17.92        78.94 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2ME 
       24.43        58.75        54.71        55.00        19.56       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A3AA 
      103.17        16.96        96.23       203.01       103.56         4.24 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A1YW TCGA-FS-A1Z4 
       44.05        79.99       216.92        28.08 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.57       112.54        28.08        65.49        58.03        60.23 
TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A29R TCGA-EE-A29T 
        6.38       117.17       176.55       215.44        14.47       345.96 
TCGA-EE-A2A0 TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       46.82       135.91        55.59        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       19.76        61.51       204.62       144.76       167.87       248.61 
TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AH TCGA-ER-A19L TCGA-FS-A1Z7 TCGA-FS-A1ZD 
      136.44       122.73       138.77       131.08         7.76        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-GN-A265 
       32.71        74.73       148.77        84.72 

$subtype4
TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-EE-A17X 
      121.22        43.40        12.10         2.70        11.34        29.82 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.65         4.93        47.84        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2GJ TCGA-EE-A2GU TCGA-EE-A2MN TCGA-EE-A2MQ 
        2.56        55.89        89.33        67.13        47.54        43.23 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-ER-A19J TCGA-FS-A1ZG 
       41.59        25.84         3.68        13.81         6.41         9.70 
TCGA-FS-A1ZJ TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       47.38        12.43        22.98       117.93        64.41        62.76 
TCGA-GN-A26D 
       39.58 

subtype1 subtype2 subtype3 subtype4 
    3.22     4.24     6.38     2.56 
subtype1 subtype2 subtype3 subtype4 
  182.01   216.92   345.96   121.22 
subtype1 subtype2 subtype3 subtype4 
  47.280   38.890   79.725   32.190 
[1] "3.2 - 182.0 (47.3)" "4.2 - 216.9 (38.9)" "6.4 - 346.0 (79.7)"
[4] "2.6 - 121.2 (32.2)"
  [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype3" "subtype3"
 [13] "subtype2" "subtype1" "subtype4" "subtype3" "subtype4" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [31] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype2" "subtype2" "subtype3" "subtype4" "subtype3"
 [43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype4" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [73] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype4"
 [79] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype4" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype3" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[103] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
[109] "subtype4" "subtype4"
  [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype3" "subtype3"
 [13] "subtype2" "subtype1" "subtype4" "subtype3" "subtype4" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [31] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype2" "subtype2" "subtype3" "subtype4" "subtype3"
 [43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype4" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [73] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype4"
 [79] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype4" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype3" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[103] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
[109] "subtype4" "subtype4"
  [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype3" "subtype3"
 [13] "subtype2" "subtype1" "subtype4" "subtype3" "subtype4" "subtype1"
 [19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [31] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype2" "subtype2" "subtype3" "subtype4" "subtype3"
 [43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype4" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [73] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype4"
 [79] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype4" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [97] "subtype3" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[103] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
[109] "subtype4" "subtype4"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  4 14
  subtype2  8 21
  subtype3 13 21
  subtype4 10 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   14
  subtype2    8   21
  subtype3   13   21
  subtype4   10   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        8       13       10
  MALE         14       21       21       21
          vv
clus       M0 M1 M1B M1C
  subtype1 17  0   1   0
  subtype2 27  0   0   0
  subtype3 29  0   1   1
  subtype4 25  1   0   0
D6V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 10  0   2   2  0   1   2   0  1  0
  subtype2 18  0   0   3  0   0   3   0  3  0
  subtype3 19  1   0   3  0   0   1   1  4  2
  subtype4 14  0   1   2  1   2   2   0  5  0
D6V5, multiclass
D6V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       1        2        2        3         0         1
  subtype2           0       6        1        3        4         2         0
  subtype3           1       6        0        3        6         2         1
  subtype4           0       2        4        3        0         1         3
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         1          1          5          0        0
  subtype2         1         0          0          4          5        0
  subtype3         0         2          0          0          6        2
  subtype4         1         1          2          1          7        1
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 21 21
  subtype2 13  9
  subtype3 19 25
subtype1 subtype2 subtype3 
      42       22       44 
subtype1 subtype2 subtype3 
      21        9       25 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.57        24.53       148.31         2.70         3.22        48.89 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 
       36.03       176.55        23.44        10.49         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       26.86         4.93        78.87        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29X TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
        2.56        17.92        58.75        43.23        22.55        89.33 
TCGA-EE-A2GT TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MS 
       19.56        16.96       144.76       167.87        47.54       136.44 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-FR-A3YN 
       41.59        25.84         3.68        26.73       138.77        80.48 
TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-GN-A268 
      216.92         9.70        47.38        74.73        49.48        62.76 

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

$subtype3
TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      121.22        43.40        65.49        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29N 
       58.03        11.34       117.17        29.82        47.84        18.58 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GH 
       14.47        55.89       345.96        78.94       135.91       182.01 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       54.71        55.00        55.59        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MR 
      103.27       103.17       204.62        96.23        43.23       103.56 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        4.24        13.81         6.41       131.08        61.05        44.05 
TCGA-ER-A1A1 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FW-A3R5 
       79.99        28.08         7.76        53.52       148.77        22.98 
TCGA-GN-A264 TCGA-GN-A267 
      117.93        64.41 

subtype1 subtype2 subtype3 
    2.56     6.38     4.24 
subtype1 subtype2 subtype3 
  216.92   248.61   345.96 
subtype1 subtype2 subtype3 
  34.880   47.410   55.295 
[1] "2.6 - 216.9 (34.9)" "6.4 - 248.6 (47.4)" "4.2 - 346.0 (55.3)"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [85] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [85] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [49] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [85] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 15 27
  subtype2  8 15
  subtype3 11 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   27
  subtype2    8   15
  subtype3   11   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15        8       11
  MALE         27       15       34
          vv
clus       M0 M1 M1B M1C
  subtype1 39  0   1   0
  subtype2 18  0   1   1
  subtype3 39  1   0   0
D7V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1 24  0   1   4  0   1   5   0  5  0
  subtype2 11  0   1   3  0   1   1   1  2  1
  subtype3 25  1   1   3  1   1   2   0  5  1
D7V5, multiclass
D7V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       4        5        4        7         1         3
  subtype2           1       2        1        0        3         1         0
  subtype3           0       9        1        7        2         3         2
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         0         0          0          6          8        0
  subtype2         2         1          1          4          1        2
  subtype3         0         3          2          0          8        1
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  7  3
  subtype2 11 14
  subtype3 35 38
subtype1 subtype2 subtype3 
      10       25       73 
subtype1 subtype2 subtype3 
       3       14       38 
$subtype1
TCGA-D3-A1Q9 TCGA-D9-A1JX TCGA-DA-A3F8 TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 
       31.59         6.38        15.68        56.42        46.82        24.43 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       47.54        67.13        28.80       203.01 

$subtype2
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
      112.54        28.08        65.49        23.77        11.87        60.23 
TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A29T TCGA-EE-A2GK TCGA-EE-A2M5 
      117.17       215.44        29.82       345.96        54.71        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3AB 
      129.24        61.51       103.17       204.62       103.56       122.73 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZS 
       44.05        79.99        28.08        53.52        32.71       148.77 
TCGA-GN-A265 
       84.72 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
       16.57       121.22        43.40        12.10        58.03        24.53 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
      148.31         2.70        11.34         3.22        48.89        36.03 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
      176.55        23.44        10.49         8.65        33.73        26.86 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.93        78.87        47.84        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 
        2.56        18.58        14.47        55.89        17.92        78.94 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        43.23       135.91       182.01        22.55        89.33 
TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       55.00        55.59        19.56        19.76        47.28       103.27 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96        96.23       144.76       167.87        47.54       248.61 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23       136.44        41.59         4.24        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       26.73        13.81       138.77        26.37         6.41       131.08 
TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1Z7 TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       61.05        80.48       216.92         7.76         9.70        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       74.73        49.48        22.98       117.93        64.41        62.76 
TCGA-GN-A26D 
       39.58 

subtype1 subtype2 subtype3 
    6.38    11.87     2.56 
subtype1 subtype2 subtype3 
  203.01   345.96   248.61 
subtype1 subtype2 subtype3 
  39.205   65.490   43.230 
[1] "6.4 - 203.0 (39.2)"  "11.9 - 346.0 (65.5)" "2.6 - 248.6 (43.2)" 
  [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
  [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
  [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [43] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  4  7
  subtype2  4 21
  subtype3 26 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    7
  subtype2    4   21
  subtype3   26   48
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        4       26
  MALE          7       21       48
          vv
clus       M0 M1 M1B M1C
  subtype1 11  0   0   0
  subtype2 20  0   1   1
  subtype3 65  1   1   0
D8V4, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  subtype1  5  0   1   2  0   1   1   0  0  1
  subtype2 13  0   0   2  0   0   0   1  5  1
  subtype3 42  1   2   6  1   2   7   0  7  0
D8V5, multiclass
D8V6, continuous
          vv
clus       I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  subtype1           0       0        1        0        2         1         0
  subtype2           1       7        1        1        1         1         1
  subtype3           0       8        5       10        9         3         4
          vv
clus       STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         1         0          1          4          0        0
  subtype2         0         1          0          0          5        2
  subtype3         1         3          2          6         12        1
D8V7, multiclass
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
