
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/8282700/KIRP-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/8142887/KIRP-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=KIRP-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KIRP-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/8142887/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/8282700/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=166, in cluster file=198, common to both=163
[1]   8 163
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
57 31 33 18 24 
 1  2  3  4  5 
57 31 33 18 24 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
31 21 28 37 30 
 1  2  3  4  5 
31 21 28 37 30 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
32 59 47 25 
 1  2  3  4 
32 59 47 25 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
58 59 46 
 1  2  3 
58 59 46 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
57 53 53 
 1  2  3 
57 53 53 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
25 63 75 
 1  2  3 
25 63 75 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
53 58 52 
 1  2  3 
53 58 52 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
58 85 20 
 1  2  3 
58 85 20 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "GLEASON_SCORE"                         
[21] "PSA_VALUE"                             
[22] "DAYS_TO_PSA"                           
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 163 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          493            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         582           27           NA            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
         140            1            2           NA           21           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
           1            3            9            1           NA           NA 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
          NA            2          118           87            4           NA 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         595          223         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         278          207            5          102         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
         270         1938           NA           NA         1454           NA 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
          NA          233           29          364           NA           84 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        3760           NA         2948         2839           NA         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
        1533         1516          799          612           NA          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
          92          876         2429         2460           NA         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
        1670         1040          578          757           97            7 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1575         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
         765          446          786          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-7128 
         112          236           32          178           91           NA 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NL TCGA-IA-A40U 
          NA           NA           NA           NA           NA          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         430           62          677          649          146            2 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
          NA            4          160          506          161          398 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E6 
         391          543          438          292          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2653           NA         2584         2816          113          174 
TCGA-Q2-A5QZ 
          57 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=128,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
[9] "YEAROFTOBACCOSMOKINGONSET"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 163 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=49, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
102  17  43   1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  102    17    44 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
102  17  43   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  102    17    44 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
27 16  4 
[1] "table(vv)"
vv
N0 N1 N2 
27 16  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
27 16  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
27 16  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=8, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=6, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 46  6
  subtype2 28  1
  subtype3 25  6
  subtype4 16  1
  subtype5 18  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      52       29       31       17       21 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        1        6        1        3 
$subtype1
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8518 
       18.21         0.69        35.18         0.23         1.61         0.10 
TCGA-A4-A5Y0 TCGA-AL-3467 TCGA-B1-5398 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4114 
        3.88        58.45        19.56        34.49        12.46        28.18 
TCGA-B9-4115 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       26.40         3.35        86.76        63.72        22.92        43.20 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-7048 
       40.83        26.04        26.04        25.35        10.88        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7838 TCGA-DW-7839 
        7.63         7.17         3.81       129.86        24.46        13.78 
TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-G7-6792 
       14.63        80.88        61.02        54.90        24.89        48.62 
TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-A4EM TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 
       25.15        12.92         1.05        14.14        22.26         0.13 
TCGA-MH-A560 TCGA-MH-A561 TCGA-P4-A5E6 TCGA-P4-A5ED 
       17.85        14.40        99.78        92.58 

$subtype2
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
       16.21        19.13         0.89         0.03         0.69         0.03 
TCGA-A4-A6HP TCGA-AL-3472 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-A5W7 
        0.13        30.35        33.83        50.50         1.15         9.14 
TCGA-BQ-7051 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7842 
       50.40        11.61        13.61        37.55         3.75         3.02 
TCGA-EV-5901 TCGA-G7-6795 TCGA-G7-A4TM TCGA-GL-A59R TCGA-IZ-8196 TCGA-IZ-A6M8 
       34.19        39.25         9.17         5.85        21.34         4.80 
TCGA-IZ-A6M9 TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
        0.07        12.85         9.60         4.87        87.22 

$subtype3
TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 
        0.10         4.60         2.86         9.63        25.08        44.61 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5876 
       10.09        20.61         0.46         6.81         0.16        19.27 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
        8.88        21.63        30.28        13.25         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6793 
       11.97       123.62        79.86        19.00         3.19        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-8500 TCGA-IA-A40Y TCGA-P4-A5EA TCGA-PJ-A5Z8 
       34.82        14.66         7.76         2.04         6.61         3.72 
TCGA-Q2-A5QZ 
        1.87 

$subtype4
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-AL-3468 
        0.07         0.07         0.76         0.30         0.03        53.79 
TCGA-B3-4103 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-7045 
       30.58        15.12        43.99        22.06        47.80        48.26 
TCGA-BQ-7060 TCGA-DW-7836 TCGA-DW-7963 TCGA-F9-A7VF TCGA-GL-6846 
        7.04        35.93        28.80         0.23       194.79 

$subtype5
TCGA-A4-A5XZ TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5893 
        0.07        13.55         7.33         2.79         2.10         7.92 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DZ-6133 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-7502 
        2.76        96.92        51.19         4.01        51.78        25.84 
TCGA-GL-7966 TCGA-GL-A59T TCGA-IA-A40U TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
        3.68         2.99        16.80         5.26        16.64         5.29 
TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 
       13.08        84.95         5.72 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.03     0.10     0.03     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.86    87.22   123.62   194.79    96.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  24.675    9.600    9.630   22.060    7.330 
[1] "0.1 - 129.9 (24.7)" "0.0 - 87.2 (9.6)"   "0.1 - 123.6 (9.6)" 
[4] "0.0 - 194.8 (22.1)" "0.1 - 96.9 (7.3)"  
  [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
  [7] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype2"
 [13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype1" "subtype4"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype4" "subtype5" "subtype2" "subtype3" "subtype3"
 [31] "subtype1" "subtype5" "subtype2" "subtype3" "subtype4" "subtype1"
 [37] "subtype1" "subtype5" "subtype2" "subtype1" "subtype1" "subtype3"
 [43] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [73] "subtype3" "subtype4" "subtype5" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype4" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [91] "subtype4" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype2" "subtype4" "subtype3" "subtype1" "subtype5" "subtype1"
[103] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
[109] "subtype5" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype1" "subtype3" "subtype5" "subtype2" "subtype4" "subtype1"
[121] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype5"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[133] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype2"
[139] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[145] "subtype3" "subtype5" "subtype1" "subtype3" "subtype5" "subtype3"
  [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
  [7] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype2"
 [13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype1" "subtype4"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype4" "subtype5" "subtype2" "subtype3" "subtype3"
 [31] "subtype1" "subtype5" "subtype2" "subtype3" "subtype4" "subtype1"
 [37] "subtype1" "subtype5" "subtype2" "subtype1" "subtype1" "subtype3"
 [43] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [73] "subtype3" "subtype4" "subtype5" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype4" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [91] "subtype4" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype2" "subtype4" "subtype3" "subtype1" "subtype5" "subtype1"
[103] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
[109] "subtype5" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype1" "subtype3" "subtype5" "subtype2" "subtype4" "subtype1"
[121] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype5"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[133] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype2"
[139] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[145] "subtype3" "subtype5" "subtype1" "subtype3" "subtype5" "subtype3"
  [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
  [7] "subtype2" "subtype1" "subtype1" "subtype4" "subtype3" "subtype2"
 [13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype1" "subtype4"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype1" "subtype4" "subtype5" "subtype2" "subtype3" "subtype3"
 [31] "subtype1" "subtype5" "subtype2" "subtype3" "subtype4" "subtype1"
 [37] "subtype1" "subtype5" "subtype2" "subtype1" "subtype1" "subtype3"
 [43] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [67] "subtype1" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [73] "subtype3" "subtype4" "subtype5" "subtype1" "subtype1" "subtype1"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype4" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [91] "subtype4" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [97] "subtype2" "subtype4" "subtype3" "subtype1" "subtype5" "subtype1"
[103] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype4"
[109] "subtype5" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype1" "subtype3" "subtype5" "subtype2" "subtype4" "subtype1"
[121] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype5"
[127] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[133] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype2"
[139] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[145] "subtype3" "subtype5" "subtype1" "subtype3" "subtype5" "subtype3"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      33        4        16        1
  subtype2      23        1         3        0
  subtype3      11        2        13        5
  subtype4      12        2         2        1
  subtype5      16        2         3        3
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 37  4    16
  subtype2 24  4     3
  subtype3 12  5    16
  subtype4 13  2     3
  subtype5 16  2     6
D1V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  8  6  1
  subtype2  4  0  0
  subtype3 10  6  2
  subtype4  3  1  0
  subtype5  2  3  1
D1V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 26  1 26
  subtype2  8  0 20
  subtype3 16  3 12
  subtype4  8  0  8
  subtype5  4  2 16
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1 20 37
  subtype2  5 26
  subtype3 14 19
  subtype4  2 16
  subtype5  8 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   37
  subtype2    5   26
  subtype3   14   19
  subtype4    2   16
  subtype5    8   16
D1V8, continuous
D1V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 subtype5 
       2        1        1        5 
[1] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
D1V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype5 
       2        1        1        2 
character(0)

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 23  5
  subtype2 12  7
  subtype3 25  2
  subtype4 32  1
  subtype5 27  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       19       27       33       27 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        7        2        1        0 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 
       18.21        35.18         0.10         0.03        44.61        19.56 
TCGA-B3-8121 TCGA-B9-A5W8 TCGA-BQ-5880 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       12.46         6.81        43.20        40.83        26.04        30.28 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7059 TCGA-BQ-7060 
       13.25        10.88        48.26        44.84         7.63         7.04 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-G7-6796 TCGA-GL-A4EM 
       24.46        28.80        80.88        61.02        34.82         1.05 
TCGA-IZ-A6M8 TCGA-KV-A6GD TCGA-P4-A5ED TCGA-PJ-A5Z8 
        4.80         5.26        92.58         3.72 

$subtype2
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-A5Y1 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.69         0.23         2.86         8.88        63.72        22.92 
TCGA-BQ-5887 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7055 TCGA-F9-A4JJ TCGA-G7-6789 
       25.35         7.92         2.76        26.27         3.19         4.01 
TCGA-G7-6793 TCGA-G7-7501 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       11.05        14.66         3.68         2.04         0.13         6.61 
TCGA-Q2-A5QZ 
        1.87 

$subtype3
TCGA-A4-7288 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5875 
       16.21         0.03         3.88         2.10         3.35        86.76 
TCGA-BQ-5876 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 
       19.27        47.80        21.63        26.04         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       11.97       123.62        93.34        61.28        50.40        49.84 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-GL-6846 TCGA-IA-A40X 
       20.12        11.28         7.17        79.86       194.79        14.14 
TCGA-IZ-8195 TCGA-MH-A560 TCGA-P4-A5EB 
       22.26        17.85        84.95 

$subtype4
TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.10         1.61         0.07         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A5XZ TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-5155 
        0.69         0.30         0.07         7.33         2.79        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-7046 TCGA-BQ-7062 TCGA-DZ-6133 
       43.99        22.06         0.16        96.92         3.81        51.19 
TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
       19.00         0.23        51.78        39.25        25.15        25.84 
TCGA-GL-8500 TCGA-GL-A59T TCGA-IA-A40U TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V 
        7.76         2.99        16.80         0.07        16.64         5.29 
TCGA-MH-A55W TCGA-P4-A5E6 TCGA-PJ-A5Z9 
       13.08        99.78         5.72 

$subtype5
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8516 TCGA-A4-A6HP TCGA-B9-A5W7 TCGA-DW-5560 
       19.13         0.89         0.76         0.13         9.14        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 
       14.63         3.02        54.90        34.19        24.89        48.62 
TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-A59R TCGA-IZ-8196 TCGA-MH-A55Z TCGA-MH-A561 
        9.17        12.92         5.85        21.34        12.85        14.40 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
        9.60         4.87        87.22 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.13     0.03     0.03     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   92.58    63.72   194.79    99.78   129.86 
subtype1 subtype2 subtype3 subtype4 subtype5 
   22.01     4.01    20.12     5.72    13.61 
[1] "0.0 - 92.6 (22.0)"  "0.1 - 63.7 (4.0)"   "0.0 - 194.8 (20.1)"
[4] "0.0 - 99.8 (5.7)"   "0.1 - 129.9 (13.6)"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype5"
  [7] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype4" "subtype5" "subtype3" "subtype1" "subtype4"
 [19] "subtype1" "subtype4" "subtype3" "subtype2" "subtype5" "subtype1"
 [25] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
 [31] "subtype4" "subtype3" "subtype5" "subtype1" "subtype4" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [73] "subtype5" "subtype5" "subtype5" "subtype5" "subtype1" "subtype5"
 [79] "subtype5" "subtype5" "subtype5" "subtype1" "subtype3" "subtype1"
 [85] "subtype4" "subtype1" "subtype5" "subtype5" "subtype4" "subtype5"
 [91] "subtype2" "subtype4" "subtype2" "subtype4" "subtype5" "subtype2"
 [97] "subtype4" "subtype1" "subtype4" "subtype2" "subtype4" "subtype5"
[103] "subtype3" "subtype5" "subtype2" "subtype4" "subtype1" "subtype5"
[109] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[115] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[121] "subtype4" "subtype5" "subtype3" "subtype5" "subtype5" "subtype5"
[127] "subtype4" "subtype5" "subtype2" "subtype3" "subtype1" "subtype1"
[133] "subtype4" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype5"
  [7] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype4" "subtype5" "subtype3" "subtype1" "subtype4"
 [19] "subtype1" "subtype4" "subtype3" "subtype2" "subtype5" "subtype1"
 [25] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
 [31] "subtype4" "subtype3" "subtype5" "subtype1" "subtype4" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [73] "subtype5" "subtype5" "subtype5" "subtype5" "subtype1" "subtype5"
 [79] "subtype5" "subtype5" "subtype5" "subtype1" "subtype3" "subtype1"
 [85] "subtype4" "subtype1" "subtype5" "subtype5" "subtype4" "subtype5"
 [91] "subtype2" "subtype4" "subtype2" "subtype4" "subtype5" "subtype2"
 [97] "subtype4" "subtype1" "subtype4" "subtype2" "subtype4" "subtype5"
[103] "subtype3" "subtype5" "subtype2" "subtype4" "subtype1" "subtype5"
[109] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[115] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[121] "subtype4" "subtype5" "subtype3" "subtype5" "subtype5" "subtype5"
[127] "subtype4" "subtype5" "subtype2" "subtype3" "subtype1" "subtype1"
[133] "subtype4" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype5"
  [7] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype4" "subtype5" "subtype3" "subtype1" "subtype4"
 [19] "subtype1" "subtype4" "subtype3" "subtype2" "subtype5" "subtype1"
 [25] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
 [31] "subtype4" "subtype3" "subtype5" "subtype1" "subtype4" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [73] "subtype5" "subtype5" "subtype5" "subtype5" "subtype1" "subtype5"
 [79] "subtype5" "subtype5" "subtype5" "subtype1" "subtype3" "subtype1"
 [85] "subtype4" "subtype1" "subtype5" "subtype5" "subtype4" "subtype5"
 [91] "subtype2" "subtype4" "subtype2" "subtype4" "subtype5" "subtype2"
 [97] "subtype4" "subtype1" "subtype4" "subtype2" "subtype4" "subtype5"
[103] "subtype3" "subtype5" "subtype2" "subtype4" "subtype1" "subtype5"
[109] "subtype4" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[115] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[121] "subtype4" "subtype5" "subtype3" "subtype5" "subtype5" "subtype5"
[127] "subtype4" "subtype5" "subtype2" "subtype3" "subtype1" "subtype1"
[133] "subtype4" "subtype2"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      22        2         4        2
  subtype2       3        1        12        5
  subtype3      10        2        13        2
  subtype4      28        3         5        0
  subtype5      27        0         2        0
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 23  1     7
  subtype2  4  1    16
  subtype3 11  3    14
  subtype4 30  4     3
  subtype5 27  1     2
D2V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  6  2  1
  subtype2  2 11  2
  subtype3 10  1  1
  subtype4  5  1  0
  subtype5  2  0  0
D2V5, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       15       12        6        2 
 [1] "subtype4" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype4" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[31] "subtype2" "subtype2" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
          vv
clus       M0 M1 MX
  subtype1 16  1 12
  subtype2  6  3 12
  subtype3 16  1  9
  subtype4  9  0 26
  subtype5  5  0 23
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1  8 23
  subtype2 14  7
  subtype3  9 19
  subtype4  9 28
  subtype5  5 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   23
  subtype2   14    7
  subtype3    9   19
  subtype4    9   28
  subtype5    5   25
D2V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        6        2       11       13 
 [1] "subtype1" "subtype1" "subtype4" "subtype4" "subtype2" "subtype1"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype5" "subtype5"
[13] "subtype5" "subtype5" "subtype5" "subtype5" "subtype1" "subtype5"
[19] "subtype5" "subtype5" "subtype5" "subtype1" "subtype5" "subtype4"
[25] "subtype5" "subtype4" "subtype2" "subtype1" "subtype4" "subtype2"
[31] "subtype4" "subtype5" "subtype4" "subtype2" "subtype2" "subtype2"
D2V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       1        3        3        2 
[1] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype4"
D2V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       1        1        2        1 
character(0)

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 29  1
  subtype2 43 12
  subtype3 40  2
  subtype4 21  2
subtype1 subtype2 subtype3 subtype4 
      30       55       42       23 
subtype1 subtype2 subtype3 subtype4 
       1       12        2        2 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8517 
       18.21        16.21        35.18         1.61         0.03         0.03 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 
        0.10         0.03         0.07        25.08        19.56         7.33 
TCGA-B3-4103 TCGA-B9-A5W8 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 
       30.58         6.81        47.80        26.04         7.66        96.92 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-DW-7963 TCGA-G7-6790 TCGA-G7-6796 TCGA-GL-A59T 
       50.40         7.04        28.80        51.78        34.82         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB 
       16.80        14.14         4.80         5.29        99.78        84.95 

$subtype2
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 
        0.69         0.23         4.60         3.88         2.86         9.63 
TCGA-AL-3467 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 
       58.45        10.09        34.49        20.61         2.10         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        3.35        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
      123.62        93.34        61.28        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 
       11.28         7.17        79.86         3.19         4.01        11.05 
TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y 
       14.66       194.79        12.92         3.68         1.05         2.04 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 
       22.26         0.13        17.85         6.61        92.58         3.72 
TCGA-Q2-A5QZ 
        1.87 

$subtype3
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 
        0.10        19.13         0.07         0.69         0.76         0.30 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-A6W5 TCGA-B9-4113 
        0.13        53.79        13.55        30.35         2.79        50.50 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 
       26.40         0.46         1.15        15.12        22.06         9.14 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       11.61        13.61        35.93        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 
        3.02        51.19        19.00         0.23        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-8500 TCGA-GL-A59R TCGA-IZ-8196 TCGA-IZ-A6M9 
       25.84         9.17         7.76         5.85        21.34         0.07 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-PJ-A5Z9 
       16.64        13.08        12.85         9.60         4.87         5.72 

$subtype4
TCGA-A4-7734 TCGA-A4-7997 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-8121 TCGA-B9-4114 
        0.89         0.07        44.61        33.83        12.46        28.18 
TCGA-B9-5156 TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7834 
       43.99        48.26        44.84         7.63         3.81       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       37.55        24.46        80.88        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-G7-6792 TCGA-KV-A6GD TCGA-MH-A561 TCGA-P4-A5E7 
       24.89        48.62         5.26        14.40        87.22 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.13     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
   99.78   194.79    53.79   129.86 
subtype1 subtype2 subtype3 subtype4 
  16.505   11.970   12.230   34.190 
[1] "0.0 - 99.8 (16.5)"  "0.1 - 194.8 (12.0)" "0.1 - 53.8 (12.2)" 
[4] "0.1 - 129.9 (34.2)"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [31] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype2"
 [37] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [43] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [85] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[103] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype4" "subtype2" "subtype3" "subtype1"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[139] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
[145] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [31] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype2"
 [37] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [43] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [85] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[103] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype4" "subtype2" "subtype3" "subtype1"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[139] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
[145] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
 [31] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype2"
 [37] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [43] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype2"
 [49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
 [85] "subtype1" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [91] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[103] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype4" "subtype2" "subtype3" "subtype1"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[139] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
[145] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      18        5         7        0
  subtype2      19        4        25        9
  subtype3      37        2         4        0
  subtype4      21        0         1        1
D3V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 20  5     7
  subtype2 22  5    32
  subtype3 38  6     3
  subtype4 22  1     2
D3V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  8  1  0
  subtype2 12 15  3
  subtype3  5  0  0
  subtype4  2  0  1
D3V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 12  0 18
  subtype2 28  6 22
  subtype3 11  0 30
  subtype4 11  0 12
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1  5 27
  subtype2 29 30
  subtype3  9 38
  subtype4  6 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   27
  subtype2   29   30
  subtype3    9   38
  subtype4    6   19
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        5       29        9        6
  MALE         27       30       38       19
D3V8, continuous
D3V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        4        1        1 
[1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
D3V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        3        2 
[1] "subtype2" "subtype2" "subtype2"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 48  3
  subtype2 51  5
  subtype3 34  9
subtype1 subtype2 subtype3 
      51       56       43 
subtype1 subtype2 subtype3 
       3        5        9 
$subtype1
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
       16.21         0.10        19.13         1.61         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A5XZ TCGA-A4-A6HP 
        0.69         0.76         0.03         0.30         0.07         0.13 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 
       53.79        13.55         7.33        30.58         2.79        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 
        9.14        48.26        50.40         3.81        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF 
       37.55         3.75        14.63        51.19        19.00         0.23 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 
       51.78        39.25        25.15        25.84       194.79         7.76 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
        5.85         2.99         0.07        16.64         5.29        13.08 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-PJ-A5Z9 
       12.85         9.60         5.72 

$subtype2
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 
       18.21        35.18         4.60         0.10         0.03         3.88 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B9-4117 TCGA-B9-A44B 
        2.86         9.63        25.08        19.56         0.46         2.10 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        6.81         0.16         3.35        86.76        19.27        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        21.63        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
       25.35         7.66         0.95        11.97       123.62        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        49.84        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 
        7.04         7.17        24.46        28.80        79.86        61.02 
TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-A4EM TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       34.82        14.66         1.05        16.80        14.14         2.04 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 TCGA-P4-A5E6 
       22.26         4.80         0.13         5.26        17.85        99.78 
TCGA-P4-A5EB TCGA-Q2-A5QZ 
       84.95         1.87 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7997 TCGA-AL-3467 TCGA-AL-3472 
        0.69         0.89         0.23         0.07        58.45        30.35 
TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4116 
       44.61        33.83        10.09        34.49        12.46        20.61 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 
        8.88        22.92        40.83        13.25        10.88         7.92 
TCGA-BQ-5894 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7839 
        2.76        44.84        26.27        11.61        35.93        13.78 
TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
        3.02        80.88        54.90        34.19        24.89         3.19 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-7966 
        4.01        48.62        11.05         9.17        12.92         3.68 
TCGA-IZ-8196 TCGA-MH-A561 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED 
       21.34        14.40         4.87        87.22         6.61        92.58 
TCGA-PJ-A5Z8 
        3.72 

subtype1 subtype2 subtype3 
    0.03     0.03     0.07 
subtype1 subtype2 subtype3 
  194.79   123.62    92.58 
subtype1 subtype2 subtype3 
   13.08    18.03    13.25 
[1] "0.0 - 194.8 (13.1)" "0.0 - 123.6 (18.0)" "0.1 - 92.6 (13.2)" 
  [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[115] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[121] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
  [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[115] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[121] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
  [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [31] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [49] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[115] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[121] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      42        5         5        1
  subtype2      26        3        26        2
  subtype3      27        3         6        7
D4V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 45  8     5
  subtype2 28  5    26
  subtype3 29  4    13
D4V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  8  1  0
  subtype2 16  8  1
  subtype3  3  7  3
D4V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 15  0 36
  subtype2 29  2 23
  subtype3 18  4 23
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1 10 48
  subtype2 15 44
  subtype3 24 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   48
  subtype2   15   44
  subtype3   24   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       15       24
  MALE         48       44       22
D4V8, continuous
D4V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        5        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        3        2 
[1] "subtype2" "subtype2" "subtype2"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 49  4
  subtype2 41  9
  subtype3 43  4
subtype1 subtype2 subtype3 
      53       50       47 
subtype1 subtype2 subtype3 
       4        9        4 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
       18.21        35.18         0.07         4.60         0.03         0.76 
TCGA-A4-A48D TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3473 TCGA-B1-5398 
        0.03         0.07         3.88         0.13        25.08        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 
        7.33        33.83        28.18        26.40         0.46        43.99 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 
        2.10         9.14         6.81        86.76        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 
       47.80        21.63        26.04        30.28        26.04         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 
        0.95        11.97       123.62        61.28        50.40        11.28 
TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 
        7.63         3.81        37.55         3.75        14.63        28.80 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-IZ-A6M8 
       79.86        54.90        51.78        48.62        14.66         4.80 
TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5E6 TCGA-P4-A5EB 
        5.29        12.85        17.85        99.78        84.95 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-A4-A5Y1 TCGA-AL-3466 
        0.69         0.89         0.23         0.10         2.86         9.63 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-4103 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 
       30.35        44.61        30.58        12.46        19.27         8.88 
TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7048 
       22.92        40.83        25.35        10.88         2.76        93.34 
TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 
       44.84        49.84        20.12         7.04         7.17        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 
       13.61       129.86        35.93        24.46        80.88        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       34.19        24.89         3.19         4.01        11.05        34.82 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-IZ-8196 
        9.17       194.79         3.68         1.05        22.26        21.34 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A561 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
        0.13         5.26        14.40         4.87        87.22         6.61 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
        3.72         1.87 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 
       16.21         0.10        19.13         1.61         0.07         0.69 
TCGA-A4-8517 TCGA-A4-8630 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3926 
        0.03         0.30        58.45        53.79        13.55        10.09 
TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
       34.49         2.79        50.50        20.61         1.15        15.12 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5888 TCGA-BQ-5893 TCGA-BQ-7045 
       22.06         0.16         3.35        13.25         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 
       96.92        26.27        13.78         3.02        51.19        19.00 
TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-7773 TCGA-GL-8500 
        0.23        39.25        25.15        25.84        12.92         7.76 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-A6M9 
        5.85         2.99        16.80        14.14         2.04         0.07 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-P4-A5ED TCGA-PJ-A5Z9 
       16.64        13.08         9.60        92.58         5.72 

subtype1 subtype2 subtype3 
    0.03     0.10     0.03 
subtype1 subtype2 subtype3 
  123.62   194.79    96.92 
subtype1 subtype2 subtype3 
  18.210   13.035   13.250 
[1] "0.0 - 123.6 (18.2)" "0.1 - 194.8 (13.0)" "0.0 - 96.9 (13.2)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[139] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      28        5        19        1
  subtype2      30        3        11        8
  subtype3      37        3         7        1
D5V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 30  8    19
  subtype2 32  3    18
  subtype3 40  6     7
D5V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 14  4  1
  subtype2  6 10  3
  subtype3  7  2  0
D5V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 24  1 25
  subtype2 22  4 27
  subtype3 16  1 30
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1 10 47
  subtype2 23 30
  subtype3 16 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   47
  subtype2   23   30
  subtype3   16   37
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       23       16
  MALE         47       30       37
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        2        5 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
D5V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 19  5
  subtype2 49  9
  subtype3 65  3
subtype1 subtype2 subtype3 
      24       58       68 
subtype1 subtype2 subtype3 
       5        9        3 
$subtype1
TCGA-A4-7585 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-B3-3925 TCGA-B9-5156 
       35.18         2.86         9.63        25.08        33.83        43.99 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5884 
        2.10        19.27         8.88        43.20        47.80        26.04 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 
        0.95        11.97        96.92        50.40        11.28         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7838 TCGA-DZ-6131 TCGA-G7-6790 TCGA-G7-7501 
        7.17         3.81        24.46        79.86        51.78        14.66 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8311 TCGA-A4-8518 TCGA-AL-3472 
        0.69         0.89         0.23         0.07         0.10        30.35 
TCGA-AL-7173 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-5155 TCGA-B9-A5W9 
       44.61        30.58        34.49        12.46        15.12         0.16 
TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
        3.35        22.92        40.83        25.35        13.25        10.88 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 
        7.92         2.76        48.26        93.34        44.84        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7842 
       26.27        20.12        11.61       129.86        35.93         3.02 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       80.88        61.02        34.19        24.89         3.19         4.01 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       11.05        34.82        25.84         9.17       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        3.68         1.05        16.80         2.04        22.26        21.34 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A561 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
        0.13         5.26        14.40         4.87        87.22         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58         3.72         5.72         1.87 

$subtype3
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 
       18.21        16.21         0.10        19.13         1.61         0.07 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
        4.60         0.03         0.69         0.76         0.03         0.30 
TCGA-A4-A48D TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.07         3.88         0.13        58.45        53.79 
TCGA-AL-3471 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 
       13.55        19.56         7.33        10.09         2.79        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 
       28.18        26.40        20.61         0.46         1.15        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5882 TCGA-BQ-5885 
        9.14         6.81        86.76        63.72        21.63        30.28 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7059 TCGA-DW-5561 
       26.04         7.66       123.62        61.28         7.63        13.61 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6133 
       37.55        13.78         3.75        14.63        28.80        51.19 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       54.90        19.00         0.23        48.62        39.25        25.15 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-IZ-A6M9 
        7.76         5.85         2.99        14.14         4.80         0.07 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 
       16.64         5.29        13.08        12.85        17.85         9.60 
TCGA-P4-A5E6 TCGA-P4-A5EB 
       99.78        84.95 

subtype1 subtype2 subtype3 
    0.95     0.07     0.03 
subtype1 subtype2 subtype3 
   96.92   194.79   123.62 
subtype1 subtype2 subtype3 
  21.865   13.825   13.580 
[1] "0.9 - 96.9 (21.9)"  "0.1 - 194.8 (13.8)" "0.0 - 123.6 (13.6)"
  [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [55] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [85] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[127] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
  [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [55] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [85] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[127] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
  [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [55] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [67] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [85] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[127] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      11        2         9        2
  subtype2      36        4        15        7
  subtype3      48        5        13        1
D6V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 13  2    10
  subtype2 37  4    22
  subtype3 52 11    12
D6V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  6  5  1
  subtype2  9  9  3
  subtype3 12  2  0
D6V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 15  2  6
  subtype2 23  3 35
  subtype3 24  1 41
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  4 21
  subtype2 27 36
  subtype3 18 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   21
  subtype2   27   36
  subtype3   18   57
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       27       18
  MALE         21       36       57
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        6        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D6V10, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 46  4
  subtype2 45 10
  subtype3 42  3
subtype1 subtype2 subtype3 
      50       55       45 
subtype1 subtype2 subtype3 
       4       10        3 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       18.21        16.21        35.18         1.61         0.07         4.60 
TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 
        0.03         0.76         0.03         0.30         0.03         3.88 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       25.08        19.56         7.33        28.18        26.40         0.46 
TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 
       43.99         2.10         3.35        86.76        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 
       47.80        21.63        26.04        30.28        26.04         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 
        0.95        11.97       123.62        96.92        61.28        50.40 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7840 TCGA-DW-7963 
       11.28         7.63         7.04         3.81         3.75        28.80 
TCGA-DZ-6131 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-IA-A40X TCGA-IZ-A6M8 
       79.86        51.78        48.62        14.66        14.14         4.80 
TCGA-MH-A560 TCGA-P4-A5EB 
       17.85        84.95 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-A4-A5Y1 TCGA-AL-3466 
        0.69         0.89         0.23         0.10         2.86         9.63 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       30.35        44.61        33.83        30.58        34.49        12.46 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 
       19.27         8.88        22.92        40.83        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 
       10.88         2.76        48.26        93.34        44.84        49.84 
TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12         7.17        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       37.55        24.46        80.88        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 
       24.89         3.19         4.01        11.05        34.82        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-IZ-8196 
        9.17       194.79         3.68         1.05        22.26        21.34 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-PJ-A5Z8 
        0.13         5.26         4.87        87.22         6.61         3.72 
TCGA-Q2-A5QZ 
        1.87 

$subtype3
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A5XZ TCGA-A4-A6HP 
        0.10        19.13         0.07         0.69         0.07         0.13 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 
       58.45        53.79        13.55        10.09         2.79        50.50 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
       20.61         1.15        15.12        22.06         9.14         6.81 
TCGA-B9-A5W9 TCGA-BQ-5893 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
        0.16         7.92        26.27        13.78        14.63         3.02 
TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-7773 
       51.19        19.00         0.23        39.25        25.15        12.92 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-A6M9 
        7.76         5.85         2.99        16.80         2.04         0.07 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
       16.64         5.29        13.08        12.85        14.40         9.60 
TCGA-P4-A5E6 TCGA-P4-A5ED TCGA-PJ-A5Z9 
       99.78        92.58         5.72 

subtype1 subtype2 subtype3 
    0.03     0.10     0.07 
subtype1 subtype2 subtype3 
  123.62   194.79    99.78 
subtype1 subtype2 subtype3 
   17.03    20.12    12.85 
[1] "0.0 - 123.6 (17.0)" "0.1 - 194.8 (20.1)" "0.1 - 99.8 (12.8)" 
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[145] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      26        3        18        1
  subtype2      33        4        12        8
  subtype3      36        4         7        1
D7V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 28  6    19
  subtype2 35  4    19
  subtype3 39  7     6
D7V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 13  3  1
  subtype2  8 10  3
  subtype3  6  3  0
D7V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 23  1 22
  subtype2 25  4 29
  subtype3 14  1 31
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1 13 40
  subtype2 24 34
  subtype3 12 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   40
  subtype2   24   34
  subtype3   12   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13       24       12
  MALE         40       34       40
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       3        2        4 
[1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
D7V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       1        2        3 
[1] "subtype3" "subtype3" "subtype3"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 43 10
  subtype2 75  2
  subtype3 15  5
subtype1 subtype2 subtype3 
      53       77       20 
subtype1 subtype2 subtype3 
      10        2        5 
$subtype1
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-4104 
        0.69         0.89         0.23        30.35        44.61        34.49 
TCGA-B3-8121 TCGA-B9-A5W9 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
       12.46         0.16         8.88        22.92        40.83        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 
       13.25        10.88         7.92         2.76        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 
       44.84        49.84        26.27        20.12        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 
       35.93        24.46         3.02        80.88        61.02        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 
       24.89         3.19         4.01        11.05        34.82        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y 
        9.17       194.79        12.92         3.68         1.05         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-KV-A6GD TCGA-MH-A561 TCGA-O9-A75Z TCGA-P4-A5E7 
       22.26        21.34         5.26        14.40         4.87        87.22 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        92.58         3.72         5.72         1.87 

$subtype2
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 
       18.21        16.21         0.10        19.13         1.61         0.07 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
        4.60         0.03         0.07         0.69         0.76         0.03 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        0.30         0.03         0.07         3.88         0.13        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 
       53.79        13.55        19.56         7.33        10.09        30.58 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        2.79        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5876 
        1.15        15.12        22.06         9.14         6.81        19.27 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 
       63.72        47.80        26.04        30.28        26.04         7.66 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.62        96.92        61.28        50.40         7.63         7.04 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3.81        13.61        37.55        13.78         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6792 
       28.80        51.19        54.90        19.00         0.23        48.62 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
       39.25        25.15         7.76         5.85         2.99        16.80 
TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       14.14         4.80         0.07        16.64         5.29        13.08 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5EB 
       12.85        17.85         9.60        99.78        84.95 

$subtype3
TCGA-A4-7585 TCGA-A4-8518 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-B3-3925 
       35.18         0.10         2.86         9.63        25.08        33.83 
TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5882 
       43.99         2.10         3.35        86.76        43.20        21.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6790 
        0.95        11.97        11.28         7.17        79.86        51.78 
TCGA-G7-7501 TCGA-J7-8537 
       14.66         0.13 

subtype1 subtype2 subtype3 
    0.16     0.03     0.10 
subtype1 subtype2 subtype3 
  194.79   123.62    86.76 
subtype1 subtype2 subtype3 
  14.400   13.780   13.315 
[1] "0.2 - 194.8 (14.4)" "0.0 - 123.6 (13.8)" "0.1 - 86.8 (13.3)" 
  [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[133] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[145] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
  [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[133] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[145] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
  [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
  [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [49] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [67] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [79] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [85] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [91] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[133] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[145] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      34        4        11        8
  subtype2      57        6        13        1
  subtype3       4        1        13        1
D8V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 35  4    19
  subtype2 61 12    12
  subtype3  6  1    13
D8V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  8  9  3
  subtype2 13  2  0
  subtype3  6  5  1
D8V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 21  4 33
  subtype2 30  1 44
  subtype3 11  1  5
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1 26 32
  subtype2 18 67
  subtype3  5 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   32
  subtype2   18   67
  subtype3    5   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26       18        5
  MALE         32       67       15
D8V8, continuous
D8V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        3        2 
[1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
D8V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        1        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
> q(save="no")
