
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/10441/12/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/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRP-TP/4467597/KIRP-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/4434786/KIRP-TP.clin.merged.picked.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/GDAC_clinicalDataPicker/KIRP-TP/4434786/KIRP-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRP-TP/4467597/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=129, in cluster file=158, common to both=129
[1]   8 129
[1] "CN_CNMF"
[1] 3
 1  2  3 
27 43 59 
 1  2  3 
27 43 59 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
31 35 47 
 1  2  3 
31 35 47 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
44 31 22 21 
 1  2  3  4 
44 31 22 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
21 58 39 
 1  2  3 
21 58 39 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
32 39 34 18 
 1  2  3  4 
32 39 34 18 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
43 33 47 
 1  2  3 
43 33 47 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
37 42 28 
 1  2  3 
37 42 28 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
10 45 52 
 1  2  3 
10 45 52 
[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] "KARNOFSKYPERFORMANCESCORE"             
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 129 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
           1           27           NA            7           49          140 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
           1            2           21           22            1            3 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3467 
          NA            1           NA           NA           NA         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1636          412          922          763         1357          595 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         223          498          307          347          334          147 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          856          803          626           14           33 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
         460          196           36           64          207            5 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        2638          585           NA         1938           NA           NA 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1454           NA         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         771          403           NA          232           29          364 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
          NA           84         3759           NA         2948         2839 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
          NA         1864         1532         1516          799          612 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
          NA          232          213          217          115          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          418 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92          876         2428         2459 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          NA         1856         1669         1040          578          757 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1574         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          445          428         5924           NA          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-7128 TCGA-HE-7129 
         235           32          178           91           NA           NA 
TCGA-HE-7130 TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
          NA          139          430           62           33          123 
TCGA-J7-6720 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
          NA          112          173 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=96,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=16,	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 129 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=45, 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 
74 16 38  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   74    16    39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
74 16 38  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   74    16    39 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
26 12  4 
[1] "table(vv)"
vv
N0 N1 N2 
26 12  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
26 12  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
26 12  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=4, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=3, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 22  2
  subtype2 34  6
  subtype3 48  7
subtype1 subtype2 subtype3 
      24       40       55 
subtype1 subtype2 subtype3 
       2        6        7 
$subtype1
TCGA-A4-7286 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-AL-3468 TCGA-AL-3471 
        0.03         0.07         0.69         0.72        53.79        13.55 
TCGA-B3-4103 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 
       11.41         1.08        15.12         6.44         1.18        47.80 
TCGA-BQ-5886 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 
       26.04        48.26        96.92         7.00         3.78        35.93 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-G7-6790 TCGA-GL-6846 TCGA-GL-A59T TCGA-PJ-A5Z9 
       28.80        51.16        51.75       194.76         2.99         5.69 

$subtype2
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.10        35.18         4.60         0.03         9.63 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 
       25.08        44.61        19.56         7.33        10.09        20.58 
TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.46         2.10         6.81        19.23         8.84        63.72 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       30.28        13.25         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-DW-7838 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-EV-5902 TCGA-G7-6789 
        2.76        24.46        79.82        80.84        19.00         4.01 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       11.05        34.82        25.15        14.63        14.07         3.68 
TCGA-GL-8500 TCGA-IA-A40U TCGA-IA-A40Y TCGA-PJ-A5Z8 
        7.73         4.57         2.04         3.68 

$subtype3
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 
       15.95         0.03         0.89         0.23         1.61         0.03 
TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3467 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4104 
        0.03         0.10        58.45        30.31        16.37        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-A5W9 TCGA-BQ-5875 
        4.83        50.50        28.14        26.40         0.16        86.73 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       22.92        43.17        21.63        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       10.88       123.58        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       49.84        26.27        20.12        11.28         7.63         7.13 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       11.61        13.61       129.86        37.55        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       14.63         3.02        61.02        54.87        34.19        24.89 
TCGA-G7-6792 TCGA-G7-6795 TCGA-GL-A4EM TCGA-GL-A59R TCGA-IA-A40X TCGA-IZ-8195 
       48.62        39.25         1.05         5.85        14.14         1.08 
TCGA-IZ-8196 
        4.04 

subtype1 subtype2 subtype3 
    0.03     0.03     0.03 
subtype1 subtype2 subtype3 
  194.76    80.84   129.86 
subtype1 subtype2 subtype3 
   12.48     9.86    20.12 
[1] "0.0 - 194.8 (12.5)" "0.0 - 80.8 (9.9)"   "0.0 - 129.9 (20.1)"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [55] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      18        2         3        1
  subtype2      16        3        14        8
  subtype3      35        5        13        1
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 19  3     5
  subtype2 17  6    20
  subtype3 38  7    14
D1V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  3  1  0
  subtype2 12  8  3
  subtype3 11  3  1
D1V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 12  0 12
  subtype2 17  5 18
  subtype3 28  1 27
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  4 23
  subtype2 16 27
  subtype3 20 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   23
  subtype2   16   27
  subtype3   20   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       16       20
  MALE         23       27       39
D1V8, continuous
D1V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 
       2        2 
character(0)
D1V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        1        1 
character(0)

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 26  3
  subtype2 24  9
  subtype3 40  1
subtype1 subtype2 subtype3 
      29       33       41 
subtype1 subtype2 subtype3 
       3        9        1 
$subtype1
TCGA-A4-7286 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-8121 
        0.03         0.10         0.03        44.61        19.56         4.83 
TCGA-B9-A5W8 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5888 TCGA-BQ-5889 
        6.81        47.80        40.83        26.04        13.25        10.88 
TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 
       48.26        44.84        49.84        26.27         7.63         7.00 
TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
        3.78        24.46        14.63        28.80        80.84        61.02 
TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6796 TCGA-GL-A4EM TCGA-PJ-A5Z8 
       24.89        48.62        34.82         1.05         3.68 

$subtype2
TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-B9-A44B TCGA-B9-A5W9 
        0.69        35.18         0.23         4.60         2.10         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       21.63        26.04        25.35         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-BQ-7058 
        7.89         2.76       123.58        93.34        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-GL-6846 
        7.13        79.82         4.01        11.05        14.63       194.76 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-IZ-8195 
        3.68         2.04         1.08 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 
       15.95         0.10         0.03         0.89         1.61         0.03 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-B1-7332 TCGA-B9-5155 
        0.07         0.69         0.72         0.03         7.33        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5885 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 
        6.44         1.18        30.28        96.92        61.28        50.37 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 
       11.61        13.61       129.86        35.93        37.55        13.74 
TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        3.75         3.02        51.16        54.87        34.19        19.00 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-8500 TCGA-GL-A59R 
       51.75        39.25        25.15        14.07         7.73         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-PJ-A5Z9 
        2.99         4.57        14.14         4.04         5.69 

subtype1 subtype2 subtype3 
    0.03     0.16     0.03 
subtype1 subtype2 subtype3 
   80.84   194.76   129.86 
subtype1 subtype2 subtype3 
   24.46    11.28    11.61 
[1] "0.0 - 80.8 (24.5)"  "0.2 - 194.8 (11.3)" "0.0 - 129.9 (11.6)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[103] "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[103] "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [85] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[103] "subtype3"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      24        2         2        2
  subtype2       6        2        20        7
  subtype3      34        3         7        0
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 25  1     5
  subtype2  6  3    26
  subtype3 36  5     6
D2V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  4  1  1
  subtype2 11 10  3
  subtype3  9  0  0
D2V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 17  1 12
  subtype2 18  4 12
  subtype3 12  0 33
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1  9 22
  subtype2 14 21
  subtype3 13 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   22
  subtype2   14   21
  subtype3   13   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       14       13
  MALE         22       21       34
D2V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       6        2       13 
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[19] "subtype3"
D2V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       1        3 
[1] "subtype3" "subtype3" "subtype3"
D2V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype3 
       2 
character(0)

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 32  9
  subtype2 25  2
  subtype3 20  2
  subtype4 17  2
subtype1 subtype2 subtype3 subtype4 
      41       27       22       19 
subtype1 subtype2 subtype3 subtype4 
       9        2        2        2 
$subtype1
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-B3-3926 
        0.69         0.23         4.60         9.63        58.45        10.09 
TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
       10.98        20.58         2.10         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.84        63.72        22.92        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        13.25        10.88         0.95         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
        2.76       123.58        93.34        49.84        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-GL-6846 
        7.13        79.82         4.01        11.05        14.63       194.76 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 TCGA-PJ-A5Z8 
        3.68         1.05         2.04         1.08         3.68 

$subtype2
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.03         1.61         0.03         0.07         0.69         0.72 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4117 
       53.79        13.55        30.31        50.50        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7839 
        1.08        15.12        11.61        13.61        35.93        13.74 
TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-8500 
       51.16        19.00        39.25        25.15        14.07         7.73 
TCGA-GL-A59R TCGA-IZ-8196 TCGA-PJ-A5Z9 
        5.85         4.04         5.69 

$subtype3
TCGA-A4-7585 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3473 TCGA-B1-5398 
       35.18         0.03         0.10         0.03        25.08        19.56 
TCGA-B9-A5W8 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5892 
        6.81        43.17        47.80        26.04         7.63        11.97 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-DW-7963 TCGA-G7-6790 
       96.92        61.28        50.37         7.00        28.80        51.75 
TCGA-G7-6796 TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
       34.82         2.99         4.57        14.14 

$subtype4
TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-5156 
       44.61        16.37        11.41         4.83        28.14         6.44 
TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7837 
       48.26        44.84         7.63         3.78       129.86        37.55 
TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       24.46        80.84        61.02        54.87        34.19        24.89 
TCGA-G7-6792 
       48.62 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.03     0.03     3.78 
subtype1 subtype2 subtype3 subtype4 
  194.76    53.79    96.92   129.86 
subtype1 subtype2 subtype3 subtype4 
   11.05    13.55    22.32    34.19 
[1] "0.2 - 194.8 (11.1)" "0.0 - 53.8 (13.6)"  "0.0 - 96.9 (22.3)" 
[4] "3.8 - 129.9 (34.2)"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype4" "subtype2" "subtype1"
 [31] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype4" "subtype3" "subtype1" "subtype4" "subtype2"
 [73] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
 [85] "subtype4" "subtype2" "subtype4" "subtype1" "subtype3" "subtype4"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype2"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype4" "subtype2" "subtype1"
 [31] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype4" "subtype3" "subtype1" "subtype4" "subtype2"
 [73] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
 [85] "subtype4" "subtype2" "subtype4" "subtype1" "subtype3" "subtype4"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype2"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype4" "subtype2" "subtype1"
 [31] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [55] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype4" "subtype3" "subtype1" "subtype4" "subtype2"
 [73] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
 [85] "subtype4" "subtype2" "subtype4" "subtype1" "subtype3" "subtype4"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[109] "subtype2"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      11        4        18        9
  subtype2      21        1         5        0
  subtype3      13        3         6        0
  subtype4      17        0         1        1
D3V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 13  5    26
  subtype2 22  5     4
  subtype3 13  3     6
  subtype4 18  1     2
D3V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 10 11  3
  subtype2  3  0  0
  subtype3  9  1  0
  subtype4  2  0  1
D3V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 23  6 13
  subtype2  8  0 19
  subtype3 13  0  9
  subtype4 10  0  9
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1 23 21
  subtype2  8 23
  subtype3  2 20
  subtype4  4 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   21
  subtype2    8   23
  subtype3    2   20
  subtype4    4   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23        8        2        4
  MALE         21       23       20       17
D3V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       4        7        2        5 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
 [7] "subtype4" "subtype4" "subtype2" "subtype4" "subtype2" "subtype4"
[13] "subtype1" "subtype2" "subtype1" "subtype2"
D3V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        1        2 
character(0)
D3V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       2        1 
character(0)

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 12  7
  subtype2 49  3
  subtype3 33  5
subtype1 subtype2 subtype3 
      19       52       38 
subtype1 subtype2 subtype3 
       7        3        5 
$subtype1
TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-4104 TCGA-BQ-5877 TCGA-BQ-5879 
        0.69         0.23        44.61        10.98         8.84        22.92 
TCGA-BQ-5883 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 
       40.83        13.25        10.88         7.89         2.76        44.84 
TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 
       80.84        34.19        24.89         4.01        11.05         3.68 
TCGA-PJ-A5Z8 
        3.68 

$subtype2
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.03         1.61         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 
        0.03        58.45        53.79        13.55        30.31        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        11.41         4.83        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A5W8 
       20.58         0.46         1.08        15.12         6.44         6.81 
TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       48.26        50.37         7.63         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DZ-6133 
      129.86        35.93        37.55        24.46        13.74        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       61.02        54.87        19.00        51.75        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A59R 
       34.82        25.15        14.07       194.76         7.73         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IZ-8196 TCGA-PJ-A5Z9 
        2.99         4.57         4.04         5.69 

$subtype3
TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3473 
       35.18         4.60         0.10         0.03         9.63        25.08 
TCGA-B1-5398 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       19.56         2.10         0.16        86.73        19.23        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        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         7.63         0.95        11.97       123.58        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 
       93.34        61.28        49.84        20.12        11.28         7.00 
TCGA-BQ-7061 TCGA-DW-7963 TCGA-DZ-6131 TCGA-G7-7501 TCGA-GL-A4EM TCGA-IA-A40X 
        7.13        28.80        79.82        14.63         1.05        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 
        2.04         1.08 

subtype1 subtype2 subtype3 
    0.23     0.03     0.03 
subtype1 subtype2 subtype3 
   80.84   194.76   123.58 
subtype1 subtype2 subtype3 
  10.980   13.905   19.840 
[1] "0.2 - 80.8 (11.0)"  "0.0 - 194.8 (13.9)" "0.0 - 123.6 (19.8)"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [97] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [97] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2"
  [1] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [61] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [97] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       8        3         3        7
  subtype2      39        3         7        1
  subtype3      15        2        20        2
D4V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  9  2    10
  subtype2 42  9     7
  subtype3 15  3    21
D4V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  2  6  3
  subtype2  7  1  0
  subtype3 15  5  1
D4V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 11  4  6
  subtype2 18  0 33
  subtype3 25  2 11
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1 14  7
  subtype2 12 46
  subtype3 11 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    7
  subtype2   12   46
  subtype3   11   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       12       11
  MALE          7       46       28
D4V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       4       12        2 
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype2"
D4V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype2 subtype3 
       3        1 
[1] "subtype2" "subtype2" "subtype2"
D4V10, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 28  2
  subtype2 30  7
  subtype3 27  2
  subtype4 13  4
subtype1 subtype2 subtype3 subtype4 
      30       37       29       17 
subtype1 subtype2 subtype3 subtype4 
       2        7        2        4 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8518 
        0.03        35.18         4.60         0.03         0.72         0.10 
TCGA-A4-A48D TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B9-5156 
        0.03        25.08        19.56         7.33        16.37         6.44 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5892 
       63.72        43.17        47.80        26.04         7.63        11.97 
TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-5561 
      123.58        61.28        50.37         7.63         3.78        13.61 
TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6135 TCGA-G7-6790 TCGA-G7-6792 
       37.55         3.75        14.63        54.87        51.75        48.62 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3466 TCGA-AL-3472 TCGA-AL-7173 
        0.69         0.89         0.23         9.63        30.31        44.61 
TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
       10.98         4.83        19.23        22.92        40.83        25.35 
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-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       20.12         7.00        11.61       129.86        35.93        24.46 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 
       80.84        61.02        34.19        24.89         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 
       34.82        14.07       194.76         3.68         1.05         1.08 
TCGA-IZ-8196 
        4.04 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 
       15.95         0.10         0.03         1.61         0.07         0.69 
TCGA-A4-8517 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 
        0.03        53.79        13.55        10.09        11.41        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
       28.14        26.40        20.58         1.08        15.12         1.18 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7055 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 
       13.25        96.92        26.27         3.02        51.16        19.00 
TCGA-G7-6797 TCGA-GL-8500 TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40Y 
       25.15         7.73         5.85         4.57         2.04 

$subtype4
TCGA-AL-3467 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 
       58.45         0.46         2.10        86.73         8.84        21.63 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7058 TCGA-BQ-7061 
       26.04        30.28         0.95         7.89        11.28         7.13 
TCGA-DW-7839 TCGA-DZ-6131 TCGA-G7-6795 TCGA-G7-7501 TCGA-IA-A40X 
       13.74        79.82        39.25        14.63        14.14 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.23     0.03     0.46 
subtype1 subtype2 subtype3 subtype4 
  123.58   194.76    96.92    86.73 
subtype1 subtype2 subtype3 subtype4 
   15.50    20.12    11.41    14.14 
[1] "0.0 - 123.6 (15.5)" "0.2 - 194.8 (20.1)" "0.0 - 96.9 (11.4)" 
[4] "0.5 - 86.7 (14.1)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [19] "subtype4" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype1"
 [49] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [61] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [67] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype4"
 [73] "subtype1" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [79] "subtype2" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [85] "subtype1" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [97] "subtype1" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [19] "subtype4" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype1"
 [49] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [61] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [67] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype4"
 [73] "subtype1" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [79] "subtype2" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [85] "subtype1" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [97] "subtype1" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [19] "subtype4" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype1" "subtype2" "subtype1" "subtype1"
 [49] "subtype4" "subtype2" "subtype4" "subtype4" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype4" "subtype1" "subtype4"
 [61] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [67] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype4"
 [73] "subtype1" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [79] "subtype2" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
 [85] "subtype1" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [97] "subtype1" "subtype2" "subtype4" "subtype2" "subtype3" "subtype4"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      17        3        10        0
  subtype2      21        4         6        7
  subtype3      21        2         6        0
  subtype4       5        0         8        3
D5V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 18  3    11
  subtype2 22  4    13
  subtype3 23  6     5
  subtype4  6  2    10
D5V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  7  2  0
  subtype2  7  6  3
  subtype3  5  1  0
  subtype4  6  3  1
D5V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 16  0 14
  subtype2 18  3 18
  subtype3 13  0 16
  subtype4  8  3  5
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1  3 29
  subtype2 16 23
  subtype3 10 24
  subtype4  9  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   29
  subtype2   16   23
  subtype3   10   24
  subtype4    9    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3       16       10        9
  MALE         29       23       24        9
D5V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       6       11        3        2 
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype3" "subtype2"
D5V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype3 subtype4 
       1        1 
character(0)
D5V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       1        1 
character(0)

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 35  6
  subtype2 28  2
  subtype3 35  7
subtype1 subtype2 subtype3 
      41       30       42 
subtype1 subtype2 subtype3 
       6        2        7 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-A48D TCGA-AL-3466 
        0.03        35.18         4.60         0.03         0.03         9.63 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B9-5156 TCGA-B9-A44B 
       25.08        19.56         7.33        16.37         6.44         2.10 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.73        19.23         8.84        63.72        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 
       21.63        26.04        30.28        26.04         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       11.97        96.92        50.37        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 
        7.13         3.78        13.61        37.55         3.75        14.63 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 
       79.82        54.87        51.75        48.62        14.63 

$subtype2
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8515 TCGA-A4-8516 
       15.95         0.10         0.03         1.61         0.69         0.72 
TCGA-A4-8517 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-4103 
        0.03        58.45        53.79        13.55        10.09        11.41 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-DW-7839 TCGA-DZ-6133 
       15.12         1.18       123.58        61.28        13.74        51.16 
TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-8500 TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40X 
       19.00        25.15         7.73         5.85         4.57        14.14 

$subtype3
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        30.31 
TCGA-AL-7173 TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
       44.61        10.98         4.83        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         7.89         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        80.84        61.02        34.19 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
       24.89         4.01        11.05        39.25        34.82        14.07 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
      194.76         3.68         1.05         2.04         1.08         4.04 

subtype1 subtype2 subtype3 
    0.03     0.03     0.07 
subtype1 subtype2 subtype3 
   96.92   123.58   194.76 
subtype1 subtype2 subtype3 
  14.630   13.645   17.095 
[1] "0.0 - 96.9 (14.6)"  "0.0 - 123.6 (13.6)" "0.1 - 194.8 (17.1)"
  [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [13] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [13] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
  [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [13] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [91] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      20        3        16        2
  subtype2      17        2         6        1
  subtype3      27        4         8        7
D6V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 21  3    19
  subtype2 20  8     5
  subtype3 28  4    15
D6V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 10  5  1
  subtype2  6  0  0
  subtype3  9  7  3
D6V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 24  2 14
  subtype2 12  1 14
  subtype3 19  3 25
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  7 36
  subtype2 11 22
  subtype3 20 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   36
  subtype2   11   22
  subtype3   20   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       11       20
  MALE         36       22       27
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 
       1        1 
character(0)
D6V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       1        1 
character(0)

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 29  4
  subtype2 33  7
  subtype3 22  2
subtype1 subtype2 subtype3 
      33       40       24 
subtype1 subtype2 subtype3 
       4        7        2 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-A48D 
        0.03        35.18         4.60         0.03         0.72         0.03 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B9-5156 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5880 
       19.56         7.33         6.44         2.10        86.73        43.17 
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         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 
        0.95        11.97       123.58        96.92        61.28        50.37 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7840 TCGA-DZ-6131 TCGA-G7-6790 
       11.28         7.63         3.78         3.75        79.82        51.75 
TCGA-G7-6792 TCGA-G7-7501 TCGA-IA-A40X 
       48.62        14.63        14.14 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-AL-7173 TCGA-B3-8121 
        0.69         0.89         0.23         0.10        44.61         4.83 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 
       19.23         8.84        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-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       20.12         7.00         7.13        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       35.93        24.46        80.84        61.02        54.87        34.19 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 
       24.89         4.01        11.05        34.82        14.07       194.76 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-IZ-8196 
        3.68         1.05         1.08         4.04 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 
       15.95         0.10         0.03         1.61         0.07         0.69 
TCGA-A4-8517 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5878 TCGA-BQ-5893 TCGA-BQ-7055 
        0.03        15.12         1.18        63.72         7.89        26.27 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 
       37.55        13.74        14.63         3.02        51.16        19.00 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-8500 TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40Y 
       39.25        25.15         7.73         5.85         4.57         2.04 

subtype1 subtype2 subtype3 
    0.03     0.10     0.03 
subtype1 subtype2 subtype3 
  123.58   194.76    63.72 
subtype1 subtype2 subtype3 
   14.63    16.65     7.81 
[1] "0.0 - 123.6 (14.6)" "0.1 - 194.8 (16.6)" "0.0 - 63.7 (7.8)"  
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[97] "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[97] "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[97] "subtype2"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      16        2        16        1
  subtype2      26        3         6        7
  subtype3      17        1         7        1
D7V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1 17  3    17
  subtype2 27  2    13
  subtype3 18  3     7
D7V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 11  2  1
  subtype2  7  6  3
  subtype3  5  3  0
D7V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 19  1 14
  subtype2 19  3 20
  subtype3  7  1 19
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1  8 29
  subtype2 18 24
  subtype3  8 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   29
  subtype2   18   24
  subtype3    8   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       18        8
  MALE         29       24       20
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        1 
character(0)
D7V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype3 
       1 
character(0)

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  6  4
  subtype2 33  8
  subtype3 45  1
subtype1 subtype2 subtype3 
      10       41       46 
subtype1 subtype2 subtype3 
       4        8        1 
$subtype1
TCGA-A4-7585 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5891 
       35.18         2.10        19.23        43.17        21.63         0.95 
TCGA-BQ-5892 TCGA-BQ-7058 TCGA-BQ-7061 TCGA-G7-7501 
       11.97        11.28         7.13        14.63 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-AL-7173 TCGA-B3-8121 
        0.69         0.89         0.23         0.10        44.61         4.83 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
        8.84        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 
        7.89         2.76        48.26        93.34        44.84        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12         7.00        11.61       129.86        35.93 
TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 
       24.46         3.02        79.82        80.84        61.02        34.19 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 
       24.89         4.01        11.05        34.82        14.07       194.76 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        3.68         1.05         2.04         1.08         4.04 

$subtype3
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8098 
        0.03        15.95         0.10         0.03         1.61         4.60 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D 
        0.03         0.07         0.69         0.72         0.03         0.03 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
       19.56         7.33        15.12         6.44         1.18        86.73 
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         7.63 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 
      123.58        96.92        61.28        50.37         7.63         3.78 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6133 
       13.61        37.55        13.74         3.75        14.63        51.16 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       54.87        19.00        51.75        48.62        39.25        25.15 
TCGA-GL-8500 TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40X 
        7.73         5.85         4.57        14.14 

subtype1 subtype2 subtype3 
    0.95     0.10     0.03 
subtype1 subtype2 subtype3 
   43.17   194.76   123.58 
subtype1 subtype2 subtype3 
   13.30    14.07    13.94 
[1] "0.9 - 43.2 (13.3)"  "0.1 - 194.8 (14.1)" "0.0 - 123.6 (13.9)"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[97] "subtype2"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[97] "subtype2"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[49] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[91] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[97] "subtype2"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3        0         7        0
  subtype2      25        3         9        8
  subtype3      31        3        13        1
D8V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  3  0     7
  subtype2 26  2    17
  subtype3 33  6    13
D8V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  4  2  1
  subtype2  8  8  3
  subtype3 11  1  0
D8V5, multiclass
          vv
clus       M0 M1 MX
  subtype1  8  0  1
  subtype2 18  4 23
  subtype3 19  1 29
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1  3  7
  subtype2 19 26
  subtype3 12 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    7
  subtype2   19   26
  subtype3   12   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3       19       12
  MALE          7       26       40
D8V8, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1       11        9 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[19] "subtype3" "subtype2"
D8V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        1 
character(0)
D8V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype3 
       1 
character(0)
> q(save="no")
