
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.73.3976/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.73.3976/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUAD/2045005/1.GDAC_mergedClustering.Finished/LUAD.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/2044090/1.GDAC_clinicalDataPicker.Finished/LUAD.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=223, in cluster file=230, common to both=223
[1]   8 223
[1] "MRNA_CNMF"
[1] 3
 1  2 
11 12 
 1  2 
11 12 
[1] "MRNA_CHIERARCHICAL"
[1] 3
1 2 3 4 5 
3 5 5 4 6 
1 2 3 4 5 
3 5 5 4 6 
[1] "CN_CNMF"
[1] 3
 1  2  3 
97 50 76 
 1  2  3 
97 50 76 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
41 45 45 43 
 1  2  3  4 
41 45 45 43 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
65 79 79 
 1  2  3 
65 79 79 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 38  51 134 
  1   2   3 
 38  51 134 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
77 92 54 
 1  2  3 
77 92 54 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
79 84 60 
 1  2  3 
79 84 60 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NEOADJUVANTTHERAPY"                    
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "STOPPEDSMOKINGYEAR"                    
[20] "TOBACCOSMOKINGHISTORYINDICATOR"        
[21] "YEAROFTOBACCOSMOKINGONSET"             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 223 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        1158          606          426           NA         1126           NA 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         303         1431           NA           NA          610           NA 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
          90          454           NA          911           NA          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
          NA          791          761          761          730           31 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
         151           NA           30           62           14         2595 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
        1147         1491          354         1357          158          574 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
         581          400          529          103          480          400 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 
          97          311          189          140          208          102 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         302          236          165           82         1938           NA 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
          NA          298           50          531          535          418 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896           NA         1314 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
         457          395          150            1           NA           NA 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        1485          455          785         1499          245          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        1091         2369          653          257          460          285 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
         135          373           NA           NA         1015           NA 
TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         255          970          418          701         1178         1374 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
           2          992           24           NA           28         1475 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
          NA           NA           67           NA           NA         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 
        1233         2161           18           34            4           95 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          40           39           31           24           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
          16           21            3         1728          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1685         1126           NA         2550            3          926 
TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1202           60           18           62           18           27 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
          21          422          154          186          690          414 
TCGA-69-7765 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 
         129           61         1599          711          911           40 
TCGA-73-4676 TCGA-75-5122 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 
         122           NA           NA           NA           NA           NA 
TCGA-75-6205 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
          NA         1093           NA         1201          760           NA 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
          NA           NA           NA         1220          678          214 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
          NA         6812           NA           NA           NA           NA 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 
          NA          327          881           NA          994           NA 
TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-91-6828 
          NA           NA           NA            7           NA           37 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
          NA           35           NA          819           28           31 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-97-7546 
         297          127           34            2          163          963 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
        1476         1331          263          181           NA           22 
TCGA-99-7458 
         250 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=143,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'STOPPEDSMOKINGYEAR':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "KARNOFSKY.PERFORMANCE.SCORE"           
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "PATHOLOGY.T"                           
 [6] "PATHOLOGY.N"                           
 [7] "PATHOLOGICSPREAD(M)"                   
 [8] "TUMOR.STAGE"                           
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NEOADJUVANT.THERAPY"                   
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "YEAROFTOBACCOSMOKINGONSET"             
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
  1   2   3   4 
115  47  47   9 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 223 columns, 1 survival variables, and 14 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 60 130  17  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 60 130  17  15 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
 T1  T2  T3  T4 
 60 130  17  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 60 130  17  15 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
132  43  41   1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  132    43    42 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
 N0  N1  N2  N3 
132  43  41   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  132    43    42 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE',vnm)"
vv
  I  II III  IV 
115  47  47   9 
[1] "table(vv)"
vv
  I  II III  IV 
115  47  47   9 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
115  47  47   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
115  47  47   9 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=64, binary=FALSE, numeric=TRUE
STOPPEDSMOKINGYEAR, nv=45, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
YEAROFTOBACCOSMOKINGONSET, nv=46, binary=FALSE, numeric=TRUE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  9  2
  subtype2 11  1
subtype1 subtype2 
      11       12 
subtype1 subtype2 
       2        1 
$subtype1
TCGA-05-4249 TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-55-1592 TCGA-55-1594 
       38.07        19.10        15.78        13.15        23.05        38.73 
TCGA-55-1596 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-67-3771 
       45.17        56.81        20.65        39.09         1.97 

$subtype2
TCGA-35-3615 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
        0.46        18.87        13.15        17.39         3.39         3.19 
TCGA-44-3919 TCGA-44-4112 TCGA-64-1680 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        6.21         4.60        37.02         0.59         2.04         0.59 

subtype1 subtype2 
    1.97     0.46 
subtype1 subtype2 
   56.81    37.02 
subtype1 subtype2 
  23.050    3.995 
[1] "2.0 - 56.8 (23.1)" "0.5 - 37.0 (4.0)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[1] "hr=" "1.7"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 4 7
  subtype2 9 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    7
  subtype2    9    3
        clus
vv       subtype1 subtype2
  FEMALE        4        9
  MALE          7        3
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       1 
character(0)
D1V5, multiclass
                                                    clus
vv                                                   subtype1 subtype2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         0        1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       11       11
D1V6, multiclass
    clus
vv   subtype1 subtype2
  T1        2        4
  T2        9        8
D1V7, multiclass
D1V8, multiclass
    clus
vv   subtype1 subtype2
  M0       11       11
  M1        0        1
D1V9, multiclass
D1V10, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2  1 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2    1   11
     clus
vv    subtype1 subtype2
  NO         0        1
  YES       11       11
D1V11, binary
          cls
clus       0 1
  subtype1 3 8
  subtype2 3 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    8
  subtype2    3    9
     clus
vv    subtype1 subtype2
  NO         3        3
  YES        8        9
D1V12, continuous
D1V13, continuous
D1V14, multiclass
D1V15, continuous

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype2 5 0
  subtype3 4 1
  subtype4 4 0
  subtype5 4 2
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        5        5        4        6 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        0        1        0        2 
$subtype1
TCGA-44-2656 TCGA-44-2659 TCGA-67-3773 
       19.10        17.39         2.04 

$subtype2
TCGA-05-4249 TCGA-44-2662 TCGA-44-2665 TCGA-44-3919 TCGA-64-1676 
       38.07        15.78        13.15         6.21        56.81 

$subtype3
TCGA-35-3615 TCGA-44-2655 TCGA-44-2666 TCGA-64-1680 TCGA-67-3774 
        0.46        18.87         3.19        37.02         0.59 

$subtype4
TCGA-44-2657 TCGA-44-2661 TCGA-44-4112 TCGA-67-3772 
       13.15         3.39         4.60         0.59 

$subtype5
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-64-1677 TCGA-64-1678 TCGA-67-3771 
       23.05        38.73        45.17        20.65        39.09         1.97 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.04     6.21     0.46     0.59     1.97 
subtype1 subtype2 subtype3 subtype4 subtype5 
   19.10    56.81    37.02    13.15    45.17 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.390   15.780    3.190    3.995   30.890 
[1] "2.0 - 19.1 (17.4)" "6.2 - 56.8 (15.8)" "0.5 - 37.0 (3.2)" 
[4] "0.6 - 13.2 (4.0)"  "2.0 - 45.2 (30.9)"
 [1] "subtype2" "subtype3" "subtype3" "subtype1" "subtype4" "subtype1"
 [7] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[13] "subtype5" "subtype5" "subtype5" "subtype2" "subtype5" "subtype5"
[19] "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
 [1] "subtype2" "subtype3" "subtype3" "subtype1" "subtype4" "subtype1"
 [7] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[13] "subtype5" "subtype5" "subtype5" "subtype2" "subtype5" "subtype5"
[19] "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
 [1] "subtype2" "subtype3" "subtype3" "subtype1" "subtype4" "subtype1"
 [7] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[13] "subtype5" "subtype5" "subtype5" "subtype2" "subtype5" "subtype5"
[19] "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 2 3
  subtype3 2 3
  subtype4 4 0
  subtype5 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    2    3
  subtype3    2    3
  subtype4    4    0
  subtype5    3    3
D2V4, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype5 
       1 
character(0)
D2V5, multiclass
D2V6, multiclass
D2V7, multiclass
D2V8, multiclass
D2V9, multiclass
D2V10, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 0 5
  subtype3 1 4
  subtype4 0 4
  subtype5 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    0    5
  subtype3    1    4
  subtype4    0    4
  subtype5    0    6
D2V11, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 2 3
  subtype3 1 4
  subtype4 1 3
  subtype5 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    2    3
  subtype3    1    4
  subtype4    1    3
  subtype5    1    5
D2V12, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        3        3        2        3 
[1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype5" "subtype2" "subtype5"
[8] "subtype5" "subtype3"
D2V13, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        1        2        2        2 
character(0)
D2V14, multiclass
D2V15, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        1        3        2        5 
[1] "subtype3" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[8] "subtype3"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 63 23
  subtype2 26 16
  subtype3 44 23
subtype1 subtype2 subtype3 
      86       42       67 
subtype1 subtype2 subtype3 
      23       16       23 
$subtype1
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4415 TCGA-05-4418 
       38.07        19.92        14.01         9.96         2.96         8.98 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-35-3615 TCGA-38-4626 
       25.02        24.00         1.02         0.99         0.46        85.32 
TCGA-38-4627 TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
       37.71        18.87        13.15         3.39        13.15         3.19 
TCGA-44-3396 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6776 
       10.22         4.60         6.84         3.35         9.93        63.72 
TCGA-44-7659 TCGA-44-7671 TCGA-44-7672 TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
        9.80        17.59        13.74        76.21        28.11        35.54 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-50-5044 
       32.84        43.20        15.02        12.99         4.93        20.48 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       25.81        49.28         8.05         8.45        15.12         4.44 
TCGA-50-6595 TCGA-55-6642 TCGA-55-6971 TCGA-55-6978 TCGA-55-6980 TCGA-55-6983 
        6.21        32.61         0.92         5.46         2.20        60.03 
TCGA-55-6986 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
       71.05         0.13         3.12         1.28         0.79         1.78 
TCGA-55-7911 TCGA-55-7914 TCGA-64-1680 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 
        0.69         0.10        37.02        39.52         2.04         0.59 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-73-4658 TCGA-73-4659 TCGA-73-4675 
        0.69         6.12        22.68        52.57        23.38         1.32 
TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
       20.58        39.48        24.99        32.09         5.88        22.29 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-91-6835 
      104.15         8.48        53.33        28.96        32.68         1.15 
TCGA-91-6849 TCGA-93-7347 TCGA-93-7348 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
        0.92         9.76         4.18        31.66        48.53        43.76 
TCGA-97-7941 TCGA-99-7458 
        0.72         8.22 

$subtype2
TCGA-05-4390 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-38-4628 TCGA-44-6774 
       37.02        14.93        30.02        25.02        49.02         5.42 
TCGA-44-6779 TCGA-44-7670 TCGA-49-4507 TCGA-49-4510 TCGA-50-5051 TCGA-50-5931 
       16.41        17.46         8.81        29.46        14.96         8.78 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5944 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 
       35.87        21.47        12.26         8.38        13.74        23.05 
TCGA-55-1594 TCGA-55-6970 TCGA-55-7576 TCGA-55-7903 TCGA-55-7907 TCGA-64-1677 
       38.73        15.25         1.32         0.62         0.53        20.65 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-67-3771 TCGA-69-7760 TCGA-69-7764 
       39.09        83.84         0.10         1.97         5.06        13.61 
TCGA-78-7145 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
       27.16        35.93        19.50        40.11         7.04        88.11 
TCGA-78-7536 TCGA-78-7542 TCGA-86-7713 TCGA-91-6828 TCGA-91-7771 TCGA-95-7043 
        8.02        10.55         0.23         1.22         1.02         0.07 

$subtype3
TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4420 TCGA-05-4426 TCGA-05-5423 
       47.05         8.02        20.05        29.95        26.01         4.96 
TCGA-05-5715 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 
        2.04        11.64        44.61         5.19        19.10        17.39 
TCGA-44-2662 TCGA-44-3919 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-7662 
       15.78         6.21         7.76         2.70        32.45         1.64 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6761 
       28.57        12.66        46.72        14.07        29.75         0.03 
TCGA-50-5049 TCGA-50-5933 TCGA-50-5941 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 
       48.82        77.88         9.37        11.05        33.37         0.72 
TCGA-53-7626 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6979 
       31.89        45.17         0.07         0.79        48.49         7.76 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 
       45.34        32.71        40.54         0.59         1.12         1.02 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3772 TCGA-67-6215 
       56.81        55.40        44.38        30.44         0.59         0.89 
TCGA-67-6217 TCGA-69-7765 TCGA-71-6725 TCGA-73-4662 TCGA-73-4676 TCGA-78-7143 
       13.87         4.24         2.01        29.95         4.01       163.10 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 
       19.27        21.86        38.50       223.96        31.20        10.75 
TCGA-91-6829 TCGA-91-6847 TCGA-95-7039 TCGA-95-7567 TCGA-97-7554 TCGA-97-7937 
       41.33        26.93         1.12         5.36         8.65         5.95 
TCGA-97-7938 
        0.59 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  104.15    88.11   223.96 
subtype1 subtype2 subtype3 
  13.070   14.945   15.780 
[1] "0.1 - 104.2 (13.1)" "0.1 - 88.1 (14.9)"  "0.0 - 224.0 (15.8)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[121] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[133] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[139] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[121] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[133] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[139] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[121] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[133] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[139] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype1"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 52 45
  subtype2 26 24
  subtype3 47 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   45
  subtype2   26   24
  subtype3   47   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       52       26       47
  MALE         45       24       29
D3V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       8        2        7 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype1"
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass
D3V9, multiclass
D3V10, binary
          cls
clus        0  1
  subtype1  5 92
  subtype2  4 46
  subtype3  6 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   92
  subtype2    4   46
  subtype3    6   70
     clus
vv    subtype1 subtype2 subtype3
  NO         5        4        6
  YES       92       46       70
D3V11, binary
          cls
clus        0  1
  subtype1 16 81
  subtype2  5 45
  subtype3 15 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   81
  subtype2    5   45
  subtype3   15   61
     clus
vv    subtype1 subtype2 subtype3
  NO        16        5       15
  YES       81       45       61
D3V12, continuous
D3V13, continuous
D3V14, multiclass
D3V15, continuous

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 29  7
  subtype2 19 19
  subtype3 30 10
  subtype4 25 11
subtype1 subtype2 subtype3 subtype4 
      36       38       40       36 
subtype1 subtype2 subtype3 subtype4 
       7       19       10       11 
$subtype1
TCGA-05-4384 TCGA-05-5423 TCGA-05-5715 TCGA-38-6178 TCGA-44-5645 TCGA-44-6146 
       14.01         4.96         2.04         5.19         6.84         9.93 
TCGA-44-6775 TCGA-44-7659 TCGA-49-4512 TCGA-50-5044 TCGA-50-5935 TCGA-50-5942 
        2.70         9.80        29.75        20.48        21.47         4.44 
TCGA-50-5944 TCGA-53-7626 TCGA-55-6543 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
       12.26        31.89         0.07        60.03        40.54        71.05 
TCGA-55-7573 TCGA-55-7725 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
        0.13         1.28         0.89         0.69        13.87         5.06 
TCGA-69-7763 TCGA-78-7143 TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-91-6849 
       22.68       163.10       104.15       223.96        53.33         0.92 
TCGA-93-7347 TCGA-93-7348 TCGA-97-7546 TCGA-97-7938 TCGA-97-7941 TCGA-99-7458 
        9.76         4.18        31.66         0.59         0.72         8.22 

$subtype2
TCGA-05-4390 TCGA-05-4396 TCGA-05-4415 TCGA-38-4631 TCGA-44-6776 TCGA-44-7670 
       37.02         9.96         2.96        11.64        63.72        17.46 
TCGA-44-7671 TCGA-49-6742 TCGA-50-5051 TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 
       17.59        15.02        14.96         8.78        35.87         8.45 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-6970 TCGA-55-6972 TCGA-64-1681 
        0.72         8.38        13.74        15.25        48.49        44.38 
TCGA-64-5774 TCGA-69-7764 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       83.84        13.61        27.16        20.58        35.93        21.86 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7166 
       19.50        38.50        32.09        40.11         7.04         8.48 
TCGA-78-7167 TCGA-78-7536 TCGA-78-7633 TCGA-86-7713 TCGA-91-6829 TCGA-91-6847 
       88.11         8.02        32.68         0.23        41.33        26.93 
TCGA-91-7771 TCGA-95-7043 
        1.02         0.07 

$subtype3
TCGA-05-4405 TCGA-05-4417 TCGA-05-4433 TCGA-05-5429 TCGA-38-4632 TCGA-44-6147 
       20.05        14.93        24.00         0.99        44.61         7.76 
TCGA-49-4488 TCGA-49-6745 TCGA-49-6761 TCGA-50-5933 TCGA-50-6597 TCGA-55-6642 
       28.57         4.93         0.03        77.88        33.37        32.61 
TCGA-55-6982 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
       32.71         0.59         1.12         1.32         1.02         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-64-5775 TCGA-69-7765 
        0.62         0.53         0.69         0.10         0.10         4.24 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4676 TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 
        2.01        52.57         4.01        19.27        39.48        24.99 
TCGA-78-7158 TCGA-78-7535 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-91-6828 
        5.88        31.20        10.75        28.96        10.55         1.22 
TCGA-95-7039 TCGA-95-7567 TCGA-97-7554 TCGA-97-7937 
        1.12         5.36         8.65         5.95 

$subtype4
TCGA-05-4424 TCGA-05-5420 TCGA-44-6145 TCGA-44-6774 TCGA-44-6777 TCGA-44-6779 
       30.02         1.02         3.35         5.42        32.45        16.41 
TCGA-44-7662 TCGA-44-7672 TCGA-49-4487 TCGA-49-4490 TCGA-49-4514 TCGA-49-6744 
        1.64        13.74        28.11        12.66        43.20        12.99 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5939 TCGA-50-5941 
       48.82        25.81        49.28         8.05        15.12         9.37 
TCGA-50-6593 TCGA-50-6595 TCGA-55-6712 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 
       11.05         6.21         0.79         0.92         5.46         7.76 
TCGA-55-6980 TCGA-55-6981 TCGA-55-7574 TCGA-55-7728 TCGA-64-1679 TCGA-64-5778 
        2.20        45.34         3.12         0.79        55.40        30.44 
TCGA-64-5781 TCGA-69-7761 TCGA-78-7160 TCGA-91-6835 TCGA-97-7552 TCGA-97-7553 
       39.52         6.12        22.29         1.15        48.53        43.76 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.03     0.79 
subtype1 subtype2 subtype3 subtype4 
  223.96    88.11    77.88    55.40 
subtype1 subtype2 subtype3 subtype4 
   9.780   17.525    5.915   12.825 
[1] "0.1 - 224.0 (9.8)" "0.1 - 88.1 (17.5)" "0.0 - 77.9 (5.9)" 
[4] "0.8 - 55.4 (12.8)"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype1"
 [19] "subtype3" "subtype4" "subtype1" "subtype2" "subtype4" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [31] "subtype3" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype4" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype1" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [67] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype1" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[133] "subtype2" "subtype4" "subtype2" "subtype1" "subtype2" "subtype1"
[139] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype4"
[145] "subtype4" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype1"
 [19] "subtype3" "subtype4" "subtype1" "subtype2" "subtype4" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [31] "subtype3" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype4" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype1" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [67] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype1" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[133] "subtype2" "subtype4" "subtype2" "subtype1" "subtype2" "subtype1"
[139] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype4"
[145] "subtype4" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype1"
 [19] "subtype3" "subtype4" "subtype1" "subtype2" "subtype4" "subtype4"
 [25] "subtype1" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [31] "subtype3" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
 [37] "subtype3" "subtype3" "subtype1" "subtype4" "subtype2" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
 [55] "subtype4" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype1" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [67] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype1"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [79] "subtype3" "subtype1" "subtype3" "subtype4" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype1" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[133] "subtype2" "subtype4" "subtype2" "subtype1" "subtype2" "subtype1"
[139] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype4"
[145] "subtype4" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 30 11
  subtype2 19 26
  subtype3 22 23
  subtype4 28 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   11
  subtype2   19   26
  subtype3   22   23
  subtype4   28   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30       19       22       28
  MALE         11       26       23       15
D4V4, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       6        2        4        2 
 [1] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [7] "subtype1" "subtype1" "subtype1" "subtype1"
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
D4V9, multiclass
D4V10, binary
          cls
clus        0  1
  subtype1  2 39
  subtype2  3 42
  subtype3  2 43
  subtype4  5 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   39
  subtype2    3   42
  subtype3    2   43
  subtype4    5   38
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        3        2        5
  YES       39       42       43       38
D4V11, binary
          cls
clus        0  1
  subtype1  8 33
  subtype2  4 41
  subtype3  8 37
  subtype4  7 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   33
  subtype2    4   41
  subtype3    8   37
  subtype4    7   36
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8        4        8        7
  YES       33       41       37       36
D4V12, continuous
D4V13, continuous
D4V14, multiclass
D4V15, continuous

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 44 12
  subtype2 41 27
  subtype3 48 23
subtype1 subtype2 subtype3 
      56       68       71 
subtype1 subtype2 subtype3 
      12       27       23 
$subtype1
TCGA-05-4249 TCGA-05-4430 TCGA-05-5423 TCGA-38-4626 TCGA-44-2655 TCGA-44-2657 
       38.07        25.02         4.96        85.32        18.87        13.15 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3919 TCGA-44-5645 TCGA-44-6147 TCGA-44-7659 
        3.39         3.19         6.21         6.84         7.76         9.80 
TCGA-49-4501 TCGA-49-4512 TCGA-50-5055 TCGA-50-5068 TCGA-50-5935 TCGA-50-5942 
       46.72        29.75        25.81        49.28        21.47         4.44 
TCGA-50-5944 TCGA-50-6593 TCGA-50-6597 TCGA-53-7626 TCGA-55-6543 TCGA-55-6985 
       12.26        11.05        33.37        31.89         0.07        40.54 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 
       71.05         1.12         0.13         3.12         1.28         1.02 
TCGA-55-7914 TCGA-64-1680 TCGA-64-1681 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        0.10        37.02        44.38         0.59         2.04         0.59 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7763 TCGA-73-4662 TCGA-73-4675 TCGA-78-7143 
        0.89        13.87        22.68        29.95         1.32       163.10 
TCGA-78-7147 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-91-6835 TCGA-91-6849 
       19.27         5.88       104.15       223.96         1.15         0.92 
TCGA-93-7347 TCGA-93-7348 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
        9.76         4.18        31.66        48.53        43.76         0.59 
TCGA-97-7941 TCGA-99-7458 
        0.72         8.22 

$subtype2
TCGA-05-4382 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4426 TCGA-38-4627 
       19.92        47.05         8.02        20.05        26.01        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
       49.02        44.61         5.19        19.10        17.39        15.78 
TCGA-44-2665 TCGA-44-3396 TCGA-44-4112 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       13.15        10.22         4.60         5.42         2.70        32.45 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7672 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       16.41         1.64        13.74        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4507 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.07         8.81        12.99         4.93         0.03        20.48 
TCGA-50-5049 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-6595 TCGA-55-6712 
       48.82         8.78        77.88         9.37         6.21         0.79 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 
        5.46         7.76         2.20        45.34        32.71         0.59 
TCGA-55-7576 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-64-1676 TCGA-64-1677 
        1.32         0.62         0.53         0.69        56.81        20.65 
TCGA-64-1679 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-67-6216 TCGA-69-7760 
       55.40         0.10        30.44        39.52         0.69         5.06 
TCGA-69-7765 TCGA-71-6725 TCGA-73-4658 TCGA-73-4676 TCGA-78-7145 TCGA-78-7155 
        4.24         2.01        52.57         4.01        27.16        38.50 
TCGA-78-7535 TCGA-78-7542 TCGA-91-6829 TCGA-91-6847 TCGA-95-7039 TCGA-95-7567 
       31.20        10.55        41.33        26.93         1.12         5.36 
TCGA-97-7554 TCGA-97-7937 
        8.65         5.95 

$subtype3
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
       14.01        37.02         9.96         2.96        14.93         8.98 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 
       29.95        30.02        25.02        24.00         1.02         0.99 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4631 TCGA-44-6145 TCGA-44-6146 TCGA-44-6776 
        2.04         0.46        11.64         3.35         9.93        63.72 
TCGA-44-7670 TCGA-44-7671 TCGA-49-4486 TCGA-49-4487 TCGA-49-4506 TCGA-49-4510 
       17.46        17.59        76.21        28.11        32.84        29.46 
TCGA-49-4514 TCGA-49-6742 TCGA-50-5051 TCGA-50-5072 TCGA-50-5932 TCGA-50-5936 
       43.20        15.02        14.96         8.05        35.87         8.45 
TCGA-50-5939 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       15.12         0.72         8.38        13.74        23.05        38.73 
TCGA-55-1596 TCGA-55-6642 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
       45.17        32.61        15.25         0.92        48.49        60.03 
TCGA-55-7728 TCGA-55-7815 TCGA-64-1678 TCGA-64-5774 TCGA-67-3771 TCGA-69-7761 
        0.79         1.78        39.09        83.84         1.97         6.12 
TCGA-69-7764 TCGA-73-4659 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       13.61        23.38        20.58        35.93        21.86        39.48 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       24.99        19.50        32.09        40.11        22.29         7.04 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        8.48        88.11         8.02        53.33        10.75        28.96 
TCGA-78-7633 TCGA-86-7713 TCGA-91-6828 TCGA-91-7771 TCGA-95-7043 
       32.68         0.23         1.22         1.02         0.07 

subtype1 subtype2 subtype3 
    0.07     0.03     0.07 
subtype1 subtype2 subtype3 
  223.96    77.88    88.11 
subtype1 subtype2 subtype3 
  10.425   12.825   17.460 
[1] "0.1 - 224.0 (10.4)" "0.0 - 77.9 (12.8)"  "0.1 - 88.1 (17.5)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [97] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[151] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[157] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[175] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[181] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[187] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[193] "subtype1" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [97] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[151] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[157] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[175] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[181] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[187] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[193] "subtype1" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [31] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
 [43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [49] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [85] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [97] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[139] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[151] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[157] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[175] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[181] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[187] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[193] "subtype1" "subtype1" "subtype1"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 50 15
  subtype2 46 33
  subtype3 29 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   15
  subtype2   46   33
  subtype3   29   50
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       46       29
  MALE         15       33       50
D5V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
      10        5        2 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1"
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
D5V9, multiclass
D5V10, binary
          cls
clus        0  1
  subtype1  5 60
  subtype2  6 73
  subtype3  4 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   60
  subtype2    6   73
  subtype3    4   75
     clus
vv    subtype1 subtype2 subtype3
  NO         5        6        4
  YES       60       73       75
D5V11, binary
          cls
clus        0  1
  subtype1 10 55
  subtype2 18 61
  subtype3  8 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   55
  subtype2   18   61
  subtype3    8   71
     clus
vv    subtype1 subtype2 subtype3
  NO        10       18        8
  YES       55       61       71
D5V12, continuous
D5V13, continuous
D5V14, multiclass
D5V15, continuous

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 19 14
  subtype2 36 11
  subtype3 78 37
subtype1 subtype2 subtype3 
      33       47      115 
subtype1 subtype2 subtype3 
      14       11       37 
$subtype1
TCGA-05-4415 TCGA-05-4418 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-38-4631 
        2.96         8.98        24.00         1.02         0.99        11.64 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6779 TCGA-44-7670 TCGA-49-4506 TCGA-49-4507 
        3.35         9.93        16.41        17.46        32.84         8.81 
TCGA-49-4514 TCGA-49-6742 TCGA-50-5072 TCGA-50-5936 TCGA-50-5939 TCGA-50-6673 
       43.20        15.02         8.05         8.45        15.12         0.72 
TCGA-55-1596 TCGA-55-6970 TCGA-55-7728 TCGA-64-5781 TCGA-67-3771 TCGA-69-7761 
       45.17        15.25         0.79        39.52         1.97         6.12 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7160 TCGA-78-7166 TCGA-78-7540 
       20.58        21.86        19.50        22.29         8.48        28.96 
TCGA-95-7043 TCGA-97-7552 TCGA-97-7941 
        0.07        48.53         0.72 

$subtype2
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 
       14.01        37.02         9.96        14.93        29.95        25.02 
TCGA-35-3615 TCGA-44-2655 TCGA-44-6774 TCGA-44-6776 TCGA-44-7671 TCGA-49-4486 
        0.46        18.87         5.42        63.72        17.59        76.21 
TCGA-49-4487 TCGA-49-4510 TCGA-50-5051 TCGA-50-5932 TCGA-50-7109 TCGA-53-7813 
       28.11        29.46        14.96        35.87         8.38        13.74 
TCGA-55-1594 TCGA-55-6642 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-7574 
       38.73        32.61         0.92        48.49        60.03         3.12 
TCGA-55-7815 TCGA-64-1678 TCGA-64-5774 TCGA-67-3774 TCGA-69-7763 TCGA-69-7764 
        1.78        39.09        83.84         0.59        22.68        13.61 
TCGA-73-4659 TCGA-73-4675 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       23.38         1.32        35.93        39.48        24.99        32.09 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 
       40.11         7.04       104.15        88.11         8.02        53.33 
TCGA-78-7633 TCGA-86-7713 TCGA-91-6828 TCGA-91-6849 TCGA-91-7771 
       32.68         0.23         1.22         0.92         1.02 

$subtype3
TCGA-05-4249 TCGA-05-4382 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4424 
       38.07        19.92        47.05         8.02        20.05        30.02 
TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5715 TCGA-38-4626 TCGA-38-4627 
       26.01        25.02         4.96         2.04        85.32        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.02        44.61         5.19        19.10        13.15        17.39 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3919 
        3.39        15.78        13.15         3.19        10.22         6.21 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 
        4.60         6.84         7.76         2.70        32.45         9.80 
TCGA-44-7662 TCGA-44-7672 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        1.64        13.74        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       14.07        29.75        12.99         4.93         0.03        20.48 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
       48.82        25.81        49.28         8.78        77.88        21.47 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
        9.37         4.44        12.26        11.05         6.21        33.37 
TCGA-53-7626 TCGA-55-1592 TCGA-55-6543 TCGA-55-6712 TCGA-55-6978 TCGA-55-6979 
       31.89        23.05         0.07         0.79         5.46         7.76 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
        2.20        45.34        32.71        40.54        71.05         0.59 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 
        1.12         0.13         1.32         1.28         1.02         0.62 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        0.53         0.69         0.10        56.81        20.65        55.40 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3772 TCGA-67-3773 
       37.02        44.38         0.10        30.44         0.59         2.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-71-6725 
        0.89         0.69        13.87         5.06         4.24         2.01 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4676 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       52.57        29.95         4.01       163.10        27.16        19.27 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 
       38.50         5.88       223.96        31.20        10.75        10.55 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6847 TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
       41.33         1.15        26.93         9.76         4.18         1.12 
TCGA-95-7567 TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        5.36        31.66        43.76         8.65         5.95         0.59 
TCGA-99-7458 
        8.22 

subtype1 subtype2 subtype3 
    0.07     0.23     0.03 
subtype1 subtype2 subtype3 
   48.53   104.15   223.96 
subtype1 subtype2 subtype3 
   11.64    23.38    12.26 
[1] "0.1 - 48.5 (11.6)"  "0.2 - 104.2 (23.4)" "0.0 - 224.0 (12.3)"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [91] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[127] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[151] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[175] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[181] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [91] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[127] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[151] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[175] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[181] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
 [91] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
 [97] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[127] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[151] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[169] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[175] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[181] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[193] "subtype3" "subtype1" "subtype3"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 15 23
  subtype2 20 31
  subtype3 90 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   23
  subtype2   20   31
  subtype3   90   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       20       90
  MALE         23       31       44
D6V4, continuous
D6V5, multiclass
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass
D6V9, multiclass
D6V10, binary
          cls
clus         0   1
  subtype1   3  35
  subtype2   3  48
  subtype3   9 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   35
  subtype2    3   48
  subtype3    9  125
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        9
  YES       35       48      125
D6V11, binary
          cls
clus         0   1
  subtype1   7  31
  subtype2   3  48
  subtype3  26 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   31
  subtype2    3   48
  subtype3   26  108
     clus
vv    subtype1 subtype2 subtype3
  NO         7        3       26
  YES       31       48      108
D6V12, continuous
D6V13, continuous
D6V14, multiclass
D6V15, continuous

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 54 18
  subtype2 48 28
  subtype3 31 16
subtype1 subtype2 subtype3 
      72       76       47 
subtype1 subtype2 subtype3 
      18       28       16 
$subtype1
TCGA-05-4384 TCGA-05-4433 TCGA-35-3615 TCGA-38-4626 TCGA-44-2661 TCGA-44-4112 
       14.01        24.00         0.46        85.32         3.39         4.60 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
        6.84         3.35         9.93        63.72        32.45         9.80 
TCGA-44-7671 TCGA-44-7672 TCGA-49-4486 TCGA-49-4487 TCGA-49-4505 TCGA-49-6744 
       17.59        13.74        76.21        28.11        14.07        12.99 
TCGA-49-6745 TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5932 TCGA-50-5936 
        4.93        20.48        14.96        25.81        35.87         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-53-7626 TCGA-55-6970 TCGA-55-6972 
        9.37         4.44        12.26        31.89        15.25        48.49 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
       71.05         0.59         1.12         0.13         1.32         1.28 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-64-1680 TCGA-67-6215 
        1.02         0.62         0.69         0.10        37.02         0.89 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-73-4676 
       13.87         6.12        22.68        13.61         4.24         4.01 
TCGA-78-7143 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
      163.10        20.58        35.93        39.48        24.99        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
       32.09         5.88        22.29       104.15         8.48        88.11 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-91-6849 TCGA-91-7771 TCGA-93-7347 
       53.33        28.96        32.68         0.92         1.02         9.76 
TCGA-95-7567 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-99-7458 
        5.36        31.66        48.53        43.76         0.59         8.22 

$subtype2
TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 
       19.92        37.02         9.96        47.05         8.02         2.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
        8.98        29.95        30.02        26.01        25.02        25.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-38-4628 TCGA-38-4632 
        1.02         4.96         0.99         2.04        49.02        44.61 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2666 TCGA-44-3396 
       19.10        13.15        17.39        15.78         3.19        10.22 
TCGA-44-3919 TCGA-44-7670 TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
        6.21        17.46        28.57        35.54        46.72        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-50-5049 TCGA-50-5068 TCGA-50-5931 
        8.81        29.46        43.20        48.82        49.28         8.78 
TCGA-50-5935 TCGA-50-6597 TCGA-50-6673 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       21.47        33.37         0.72        13.74        23.05        38.73 
TCGA-55-1596 TCGA-55-6971 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-7728 
       45.17         0.92         7.76         2.20        45.34         0.79 
TCGA-55-7907 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 
        0.53        56.81        20.65        39.09        44.38        83.84 
TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        0.10        30.44         1.97         0.59         2.04         0.59 
TCGA-73-4659 TCGA-73-4662 TCGA-78-7147 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
       23.38        29.95        19.27        38.50        40.11         7.04 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-86-7713 TCGA-91-6828 TCGA-91-6835 
        8.02        10.75        10.55         0.23         1.22         1.15 
TCGA-91-6847 TCGA-95-7039 TCGA-95-7043 TCGA-97-7941 
       26.93         1.12         0.07         0.72 

$subtype3
TCGA-05-4249 TCGA-05-4405 TCGA-05-4417 TCGA-38-4627 TCGA-38-4631 TCGA-38-6178 
       38.07        20.05        14.93        37.71        11.64         5.19 
TCGA-44-2655 TCGA-44-2665 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6779 
       18.87        13.15         7.76         5.42         2.70        16.41 
TCGA-44-7662 TCGA-49-4490 TCGA-49-4512 TCGA-49-6742 TCGA-49-6761 TCGA-50-5072 
        1.64        12.66        29.75        15.02         0.03         8.05 
TCGA-50-5933 TCGA-50-5939 TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 TCGA-55-6543 
       77.88        15.12        11.05         6.21         8.38         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6978 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
       32.61         0.79         5.46        32.71        60.03        40.54 
TCGA-55-7574 TCGA-55-7815 TCGA-64-1679 TCGA-64-5781 TCGA-67-6216 TCGA-69-7760 
        3.12         1.78        55.40        39.52         0.69         5.06 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4675 TCGA-78-7145 TCGA-78-7150 TCGA-78-7163 
        2.01        52.57         1.32        27.16        21.86       223.96 
TCGA-78-7535 TCGA-91-6829 TCGA-93-7348 TCGA-97-7554 TCGA-97-7937 
       31.20        41.33         4.18         8.65         5.95 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  163.10    83.84   223.96 
subtype1 subtype2 subtype3 
  13.805   17.425   12.660 
[1] "0.1 - 163.1 (13.8)" "0.1 - 83.8 (17.4)"  "0.0 - 224.0 (12.7)"
  [1] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[151] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[181] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[187] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype1" "subtype2" "subtype1"
  [1] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[151] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[181] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[187] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype1" "subtype2" "subtype1"
  [1] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
 [13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [49] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [73] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [97] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
[121] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[139] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[151] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[163] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[175] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[181] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[187] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[193] "subtype1" "subtype2" "subtype1"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 40 37
  subtype2 53 39
  subtype3 32 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   37
  subtype2   53   39
  subtype3   32   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       53       32
  MALE         37       39       22
D7V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       8        7        2 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1"
D7V5, multiclass
D7V6, multiclass
D7V7, multiclass
D7V8, multiclass
D7V9, multiclass
D7V10, binary
          cls
clus        0  1
  subtype1  6 71
  subtype2  5 87
  subtype3  4 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   71
  subtype2    5   87
  subtype3    4   50
     clus
vv    subtype1 subtype2 subtype3
  NO         6        5        4
  YES       71       87       50
D7V11, binary
          cls
clus        0  1
  subtype1 14 63
  subtype2  9 83
  subtype3 13 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   63
  subtype2    9   83
  subtype3   13   41
     clus
vv    subtype1 subtype2 subtype3
  NO        14        9       13
  YES       63       83       41
D7V12, continuous
D7V13, continuous
D7V14, multiclass
D7V15, continuous

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 38 27
  subtype2 60 19
  subtype3 35 16
subtype1 subtype2 subtype3 
      65       79       51 
subtype1 subtype2 subtype3 
      27       19       16 
$subtype1
TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 
       19.92        37.02         9.96        47.05         8.02         2.96 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
       14.93         8.98        29.95        30.02        25.02        25.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 
        1.02         4.96         2.04        49.02        11.64        44.61 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2666 TCGA-44-3396 TCGA-44-7670 TCGA-49-4488 
       19.10        17.39         3.19        10.22        17.46        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 
       12.66        35.54        46.72        32.84         8.81        15.02 
TCGA-50-5049 TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 TCGA-50-5939 TCGA-50-6673 
       48.82         8.05         8.78        21.47        15.12         0.72 
TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-7815 
        8.38        13.74        23.05        38.73        45.17         1.78 
TCGA-55-7907 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 
        0.53        20.65        39.09        55.40        83.84         0.10 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-69-7760 TCGA-73-4659 TCGA-73-4662 
        1.97         0.59         2.04         5.06        23.38        29.95 
TCGA-78-7150 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7536 TCGA-78-7539 
       21.86        38.50        40.11         7.04         8.02        10.75 
TCGA-78-7542 TCGA-86-7713 TCGA-91-6828 TCGA-91-6829 TCGA-95-7039 
       10.55         0.23         1.22        41.33         1.12 

$subtype2
TCGA-05-4384 TCGA-05-4426 TCGA-05-4433 TCGA-35-3615 TCGA-38-4626 TCGA-44-2657 
       14.01        26.01        24.00         0.46        85.32        13.15 
TCGA-44-2661 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
        3.39         6.21         4.60         6.84         3.35         9.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7671 TCGA-44-7672 
        7.76        63.72        32.45         9.80        17.59        13.74 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4505 TCGA-49-4510 TCGA-49-4514 TCGA-49-6745 
       76.21        28.11        14.07        29.46        43.20         4.93 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5932 TCGA-50-5936 TCGA-50-5941 
       20.48        14.96        25.81        35.87         8.45         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-53-7626 TCGA-55-6970 TCGA-55-6972 
        4.44        12.26        33.37        31.89        15.25        48.49 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
       71.05         0.59         1.12         0.13         1.32         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7911 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
        1.02         0.79         0.69        37.02        44.38        30.44 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        0.59         0.89        13.87         6.12        22.68        13.61 
TCGA-69-7765 TCGA-73-4675 TCGA-73-4676 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        4.24         1.32         4.01        19.27        20.58        35.93 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
       39.48        24.99        19.50        32.09         5.88        22.29 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7540 TCGA-78-7633 TCGA-91-6835 
      104.15         8.48        88.11        28.96        32.68         1.15 
TCGA-91-7771 TCGA-93-7347 TCGA-95-7567 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
        1.02         9.76         5.36        48.53        43.76         0.59 
TCGA-99-7458 
        8.22 

$subtype3
TCGA-05-4249 TCGA-05-4405 TCGA-05-5429 TCGA-38-4627 TCGA-38-6178 TCGA-44-2655 
       38.07        20.05         0.99        37.71         5.19        18.87 
TCGA-44-2662 TCGA-44-2665 TCGA-44-6774 TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 
       15.78        13.15         5.42         2.70        16.41         1.64 
TCGA-49-4512 TCGA-49-6744 TCGA-49-6761 TCGA-50-5068 TCGA-50-5933 TCGA-50-6593 
       29.75        12.99         0.03        49.28        77.88        11.05 
TCGA-50-6595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6978 
        6.21         0.07        32.61         0.79         0.92         5.46 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
        7.76         2.20        45.34        32.71        60.03        40.54 
TCGA-55-7574 TCGA-55-7903 TCGA-55-7914 TCGA-64-1676 TCGA-64-5781 TCGA-67-6216 
        3.12         0.62         0.10        56.81        39.52         0.69 
TCGA-71-6725 TCGA-73-4658 TCGA-78-7143 TCGA-78-7145 TCGA-78-7163 TCGA-78-7535 
        2.01        52.57       163.10        27.16       223.96        31.20 
TCGA-78-7537 TCGA-91-6847 TCGA-91-6849 TCGA-93-7348 TCGA-95-7043 TCGA-97-7546 
       53.33        26.93         0.92         4.18         0.07        31.66 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        8.65         5.95         0.72 

subtype1 subtype2 subtype3 
    0.10     0.13     0.03 
subtype1 subtype2 subtype3 
   83.84   104.15   223.96 
subtype1 subtype2 subtype3 
   15.02    13.87    12.99 
[1] "0.1 - 83.8 (15.0)"  "0.1 - 104.2 (13.9)" "0.0 - 224.0 (13.0)"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[139] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[151] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[163] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[175] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[181] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[187] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[193] "subtype2" "subtype3" "subtype2"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[139] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[151] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[163] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[175] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[181] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[187] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[193] "subtype2" "subtype3" "subtype2"
  [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [31] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [61] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[127] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[139] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[151] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[157] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[163] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[175] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[181] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[187] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[193] "subtype2" "subtype3" "subtype2"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 39 40
  subtype2 45 39
  subtype3 41 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   40
  subtype2   45   39
  subtype3   41   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39       45       41
  MALE         40       39       19
D8V4, continuous
D8V5, multiclass
D8V6, multiclass
D8V7, multiclass
D8V8, multiclass
D8V9, multiclass
D8V10, binary
          cls
clus        0  1
  subtype1  7 72
  subtype2  6 78
  subtype3  2 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   72
  subtype2    6   78
  subtype3    2   58
     clus
vv    subtype1 subtype2 subtype3
  NO         7        6        2
  YES       72       78       58
D8V11, binary
          cls
clus        0  1
  subtype1 12 67
  subtype2 13 71
  subtype3 11 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   67
  subtype2   13   71
  subtype3   11   49
     clus
vv    subtype1 subtype2 subtype3
  NO        12       13       11
  YES       67       71       49
D8V12, continuous
D8V13, continuous
D8V14, multiclass
D8V15, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
           "KARNOFSKY.PERFORMANCE.SCORE" 
                                      V5 
                     "HISTOLOGICAL.TYPE" 
                                      V6 
                           "PATHOLOGY.T" 
                                      V7 
                           "PATHOLOGY.N" 
                                      V8 
                   "PATHOLOGICSPREAD(M)" 
                                      V9 
                           "TUMOR.STAGE" 
                                     V10 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V11 
                   "NEOADJUVANT.THERAPY" 
                                     V12 
                 "NUMBERPACKYEARSSMOKED" 
                                     V13 
                    "STOPPEDSMOKINGYEAR" 
                                     V14 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
                                     V15 
             "YEAROFTOBACCOSMOKINGONSET" 
> q(save="no")
