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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/6159655/BLCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/6154386/BLCA-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=BLCA-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=BLCA-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/6154386/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/6159655/BLCA-TP.mergedcluster.txt"

nPatients in clinical file=186, in cluster file=242, common to both=186
[1]  10 186
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5  6  7  8 
16 67 16 11 31 21 12  9 
 1  2  3  4  5  6  7  8 
16 67 16 11 31 21 12  9 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
66 75 45 
 1  2  3 
66 75 45 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
36 28 36  5 20 
 1  2  3  4  5 
36 28 36  5 20 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
41 18 23 43 
 1  2  3  4 
41 18 23 43 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
26 56 38 66 
 1  2  3  4 
26 56 38 66 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
76 32 78 
 1  2  3 
76 32 78 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
43 81 61 
 1  2  3 
43 81 61 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
124  17  44 
  1   2   3 
124  17  44 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
30 50 58 47 
 1  2  3  4 
30 50 58 47 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
50 59 45 31 
 1  2  3  4 
50 59 45 31 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "GLEASON_SCORE"                         
[21] "PSA_VALUE"                             
[22] "DAYS_TO_PSA"                           
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 186 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        1219           NA           NA           NA          197           NA 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
         363           NA           NA           NA           NA           NA 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
         521          170          111           NA          390           63 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
         304           NA           59           88          700           NA 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
          14           13           21           NA           NA           NA 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
          NA            4            2            3            2            3 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
           3           NA           NA          219          166          158 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
         495           NA           77           NA          955          560 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
         578          271         3980         3420          491          536 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
         475           55          322           NA         3767         2655 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
          67          121          238           NA          319         1529 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
         648          609           NA          252           NA         4283 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
        1460           NA         1326           NA          796          407 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
           3           15           16           NA           17           17 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
          20           42           25          392          477           NA 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
         209           NA          378          363          483         1397 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
          NA          683          501          390           NA          401 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
          NA           NA           59          699          453          455 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
         454          110          369          406         1130           NA 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
         209           NA           NA          208           NA          209 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z7 
        1510           81          146           NA          193          461 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
         216          106          124           NA          196          679 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        1884          931          172           NA         1072          525 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
         214           NA           25           87           68          481 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
         137          483          428          539           33          234 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
          64           95          638          194          232          344 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG 
         133          195          187          173          232           NA 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
         237          125          202          194          580           46 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
         204           NA          265          104          141           76 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
         197           55          130          192          104          112 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=121,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=20,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "NUMBER.OF.LYMPH.NODES"       "GLEASON_SCORE"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 186 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1  1 51 88 27 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      53       88       27 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1  1 51 88 27 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      53       88       27 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
114  17  33   6 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
114  17  33   6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
114  17  33   6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
114  17  33   6 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=45, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=13, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 11  5
  subtype2 46 18
  subtype3 10  6
  subtype4  8  3
  subtype5 22  7
  subtype6 14  7
  subtype7  5  5
  subtype8  6  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      16       64       16       11       29       21       10        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       5       18        6        3        7        7        5        3 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-CU-A0YR TCGA-DK-A1A6 TCGA-DK-A3IK TCGA-DK-A3IM 
       40.08         2.66         7.20        31.40         2.20         7.82 
TCGA-FD-A5BR TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-G2-A2EO TCGA-G2-A3IE 
       13.35         4.80         6.25         6.35        35.24        20.12 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A40E TCGA-K4-A4AC 
        4.37         7.79         6.38         6.48 

$subtype2
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.48         6.58        11.93        19.00        12.16 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-C4-A0F0 
       19.46        14.89        14.93         8.25         2.07         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AA TCGA-DK-A1AE 
        0.10         4.90        16.27         1.84        19.00        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
       17.62        15.62        10.49        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       10.55       140.81        13.38         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM 
        1.38         0.82        15.68        12.43        15.88        16.47 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        5.49        13.18        46.78        14.96        14.93         3.62 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EJ 
       37.15         6.87         5.69         7.10         3.48        30.61 
TCGA-G2-A2EK TCGA-G2-A3IB TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GU-A42Q 
        5.65         7.04        15.81        17.72         3.12         7.63 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51         8.71         3.42         2.50 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20R TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-FD-A3B6 
        6.74         5.06         5.19         7.76       123.85         6.87 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A5BT TCGA-FD-A62N TCGA-G2-A2EL TCGA-GD-A3OP 
        4.01        22.45        11.01         2.66        26.93         2.10 
TCGA-GV-A3JX TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
        6.15         1.81         6.31         3.42 

$subtype4
TCGA-BT-A20N TCGA-BT-A20V TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A3IL 
       32.84         5.06        18.41       130.85        10.59         3.98 
TCGA-DK-A3X1 TCGA-FD-A43P TCGA-FJ-A3Z7 TCGA-GV-A3QI TCGA-GV-A40G 
       48.00        14.89        15.16         4.11        19.07 

$subtype5
TCGA-BT-A20P TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB 
       17.85         9.99        23.01         5.46         2.14         8.91 
TCGA-DK-A3IV TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3SN 
        9.67        26.17         0.56         0.56         8.94        12.82 
TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.79        12.13         5.36         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FT-A61P TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OS 
       49.64         6.44        15.88        14.07         7.69        20.98 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-K4-A3WV TCGA-MV-A51V 
       11.31         6.41         6.71         4.64         3.68 

$subtype6
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A1HS 
        8.35        17.13         3.65        12.82         8.98         0.43 
TCGA-CU-A0YN TCGA-DK-A1AD TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-FD-A3B3 TCGA-FD-A3N5 
       12.92       112.44        15.32         0.49        12.89        11.93 
TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A3VY TCGA-GC-A3RB 
       24.30        22.98         4.08        61.94         0.82         4.50 
TCGA-GC-A3YS TCGA-GV-A3JZ TCGA-K4-A6MB 
        1.08         5.69         4.27 

$subtype7
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-DK-A1A3 TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
        5.59         4.64         2.53         1.81        87.29         8.22 
TCGA-FT-A3EE TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A3QK 
        3.22         6.38         7.63         6.64 

$subtype8
TCGA-CF-A47X TCGA-DK-A3IS TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SS 
        0.10        50.27        17.98        43.59        45.93         1.94 
TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         2.86         2.24 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    2.20     0.07     1.81     3.98     0.56     0.43     1.81     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   40.08   140.81   123.85   130.85    49.64   112.44    87.29    50.27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   6.840    7.940    6.230   15.160    8.940    8.980    5.985   17.260 
[1] "2.2 - 40.1 (6.8)"   "0.1 - 140.8 (7.9)"  "1.8 - 123.8 (6.2)" 
[4] "4.0 - 130.8 (15.2)" "0.6 - 49.6 (8.9)"   "0.4 - 112.4 (9.0)" 
[7] "1.8 - 87.3 (6.0)"   "0.1 - 50.3 (17.3)" 
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
 [13] "subtype3" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [19] "subtype6" "subtype7" "subtype6" "subtype7" "subtype6" "subtype2"
 [25] "subtype5" "subtype6" "subtype2" "subtype5" "subtype2" "subtype6"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype8"
 [37] "subtype2" "subtype6" "subtype2" "subtype1" "subtype5" "subtype3"
 [43] "subtype2" "subtype2" "subtype7" "subtype5" "subtype1" "subtype4"
 [49] "subtype2" "subtype5" "subtype4" "subtype6" "subtype2" "subtype2"
 [55] "subtype2" "subtype7" "subtype4" "subtype3" "subtype3" "subtype7"
 [61] "subtype1" "subtype4" "subtype1" "subtype7" "subtype2" "subtype8"
 [67] "subtype2" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
 [73] "subtype4" "subtype8" "subtype8" "subtype6" "subtype5" "subtype2"
 [79] "subtype2" "subtype6" "subtype2" "subtype5" "subtype5" "subtype2"
 [85] "subtype2" "subtype2" "subtype6" "subtype2" "subtype5" "subtype3"
 [91] "subtype3" "subtype2" "subtype6" "subtype2" "subtype8" "subtype6"
 [97] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[103] "subtype5" "subtype8" "subtype6" "subtype4" "subtype2" "subtype2"
[109] "subtype2" "subtype5" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype5" "subtype2" "subtype5" "subtype5" "subtype5" "subtype5"
[121] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2" "subtype6" "subtype7" "subtype5" "subtype6" "subtype2"
[133] "subtype2" "subtype3" "subtype1" "subtype8" "subtype2" "subtype1"
[139] "subtype6" "subtype8" "subtype8" "subtype2" "subtype6" "subtype5"
[145] "subtype5" "subtype2" "subtype6" "subtype5" "subtype3" "subtype2"
[151] "subtype5" "subtype7" "subtype2" "subtype5" "subtype1" "subtype5"
[157] "subtype3" "subtype6" "subtype7" "subtype1" "subtype4" "subtype7"
[163] "subtype1" "subtype4" "subtype2" "subtype5" "subtype2" "subtype2"
[169] "subtype5" "subtype2" "subtype1" "subtype3" "subtype6" "subtype3"
[175] "subtype3" "subtype5"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
 [13] "subtype3" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [19] "subtype6" "subtype7" "subtype6" "subtype7" "subtype6" "subtype2"
 [25] "subtype5" "subtype6" "subtype2" "subtype5" "subtype2" "subtype6"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype8"
 [37] "subtype2" "subtype6" "subtype2" "subtype1" "subtype5" "subtype3"
 [43] "subtype2" "subtype2" "subtype7" "subtype5" "subtype1" "subtype4"
 [49] "subtype2" "subtype5" "subtype4" "subtype6" "subtype2" "subtype2"
 [55] "subtype2" "subtype7" "subtype4" "subtype3" "subtype3" "subtype7"
 [61] "subtype1" "subtype4" "subtype1" "subtype7" "subtype2" "subtype8"
 [67] "subtype2" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
 [73] "subtype4" "subtype8" "subtype8" "subtype6" "subtype5" "subtype2"
 [79] "subtype2" "subtype6" "subtype2" "subtype5" "subtype5" "subtype2"
 [85] "subtype2" "subtype2" "subtype6" "subtype2" "subtype5" "subtype3"
 [91] "subtype3" "subtype2" "subtype6" "subtype2" "subtype8" "subtype6"
 [97] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[103] "subtype5" "subtype8" "subtype6" "subtype4" "subtype2" "subtype2"
[109] "subtype2" "subtype5" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype5" "subtype2" "subtype5" "subtype5" "subtype5" "subtype5"
[121] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2" "subtype6" "subtype7" "subtype5" "subtype6" "subtype2"
[133] "subtype2" "subtype3" "subtype1" "subtype8" "subtype2" "subtype1"
[139] "subtype6" "subtype8" "subtype8" "subtype2" "subtype6" "subtype5"
[145] "subtype5" "subtype2" "subtype6" "subtype5" "subtype3" "subtype2"
[151] "subtype5" "subtype7" "subtype2" "subtype5" "subtype1" "subtype5"
[157] "subtype3" "subtype6" "subtype7" "subtype1" "subtype4" "subtype7"
[163] "subtype1" "subtype4" "subtype2" "subtype5" "subtype2" "subtype2"
[169] "subtype5" "subtype2" "subtype1" "subtype3" "subtype6" "subtype3"
[175] "subtype3" "subtype5"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype4" "subtype2" "subtype5" "subtype2"
 [13] "subtype3" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [19] "subtype6" "subtype7" "subtype6" "subtype7" "subtype6" "subtype2"
 [25] "subtype5" "subtype6" "subtype2" "subtype5" "subtype2" "subtype6"
 [31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype8"
 [37] "subtype2" "subtype6" "subtype2" "subtype1" "subtype5" "subtype3"
 [43] "subtype2" "subtype2" "subtype7" "subtype5" "subtype1" "subtype4"
 [49] "subtype2" "subtype5" "subtype4" "subtype6" "subtype2" "subtype2"
 [55] "subtype2" "subtype7" "subtype4" "subtype3" "subtype3" "subtype7"
 [61] "subtype1" "subtype4" "subtype1" "subtype7" "subtype2" "subtype8"
 [67] "subtype2" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
 [73] "subtype4" "subtype8" "subtype8" "subtype6" "subtype5" "subtype2"
 [79] "subtype2" "subtype6" "subtype2" "subtype5" "subtype5" "subtype2"
 [85] "subtype2" "subtype2" "subtype6" "subtype2" "subtype5" "subtype3"
 [91] "subtype3" "subtype2" "subtype6" "subtype2" "subtype8" "subtype6"
 [97] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[103] "subtype5" "subtype8" "subtype6" "subtype4" "subtype2" "subtype2"
[109] "subtype2" "subtype5" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype5" "subtype2" "subtype5" "subtype5" "subtype5" "subtype5"
[121] "subtype3" "subtype1" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2" "subtype6" "subtype7" "subtype5" "subtype6" "subtype2"
[133] "subtype2" "subtype3" "subtype1" "subtype8" "subtype2" "subtype1"
[139] "subtype6" "subtype8" "subtype8" "subtype2" "subtype6" "subtype5"
[145] "subtype5" "subtype2" "subtype6" "subtype5" "subtype3" "subtype2"
[151] "subtype5" "subtype7" "subtype2" "subtype5" "subtype1" "subtype5"
[157] "subtype3" "subtype6" "subtype7" "subtype1" "subtype4" "subtype7"
[163] "subtype1" "subtype4" "subtype2" "subtype5" "subtype2" "subtype2"
[169] "subtype5" "subtype2" "subtype1" "subtype3" "subtype6" "subtype3"
[175] "subtype3" "subtype5"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        6         4        5
  subtype2       1       24        27       13
  subtype3       0        3         7        6
  subtype4       0        3         4        4
  subtype5       0       11        10        9
  subtype6       0        5         7        8
  subtype7       0        1         4        7
  subtype8       0        5         1        3
D1V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1        6  6  1
  subtype2       21 30 11
  subtype3        2  9  3
  subtype4        3  6  2
  subtype5       10 14  3
  subtype6        4 12  2
  subtype7        2  7  3
  subtype8        5  3  1
D1V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1  6  2  4  0
  subtype2 51  4  7  2
  subtype3  9  2  3  1
  subtype4  7  0  4  0
  subtype5 18  2  5  0
  subtype6 10  4  3  2
  subtype7  5  2  5  0
  subtype8  6  1  1  1
D1V5, multiclass
          vv
clus       M0 M1 MX
  subtype1  7  0  9
  subtype2 39  2 26
  subtype3  6  1  9
  subtype4  6  0  5
  subtype5 13  1 17
  subtype6 11  1  8
  subtype7  9  0  3
  subtype8  6  0  3
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  1 15
  subtype2 14 53
  subtype3  4 12
  subtype4  5  6
  subtype5 13 18
  subtype6  4 17
  subtype7  4  8
  subtype8  1  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   15
  subtype2   14   53
  subtype3    4   12
  subtype4    5    6
  subtype5   13   18
  subtype6    4   17
  subtype7    4    8
  subtype8    1    8
D1V8, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       5       13        2        2        9        6        6        6 
 [1] "subtype6" "subtype2" "subtype7" "subtype5" "subtype2" "subtype7"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype8" "subtype2"
[13] "subtype7" "subtype7" "subtype5" "subtype2" "subtype8" "subtype8"
[19] "subtype6" "subtype5" "subtype2" "subtype5" "subtype5" "subtype6"
[25] "subtype2" "subtype2" "subtype1" "subtype8" "subtype2" "subtype1"
[31] "subtype6" "subtype8" "subtype8" "subtype2" "subtype5" "subtype5"
[37] "subtype6" "subtype5" "subtype1" "subtype5" "subtype6" "subtype7"
[43] "subtype1" "subtype7" "subtype1"
D1V9, continuous
D1V10, continuous
D1V11, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       4       12        2        3        6        5        4        3 
 [1] "subtype4" "subtype2" "subtype6" "subtype6" "subtype6" "subtype2"
 [7] "subtype1" "subtype5" "subtype2" "subtype4" "subtype7" "subtype7"
[13] "subtype8" "subtype2" "subtype2" "subtype5" "subtype8" "subtype5"
[19] "subtype2" "subtype5" "subtype4" "subtype5" "subtype1" "subtype2"
[25] "subtype2" "subtype5" "subtype1" "subtype8" "subtype6" "subtype6"
[31] "subtype7" "subtype7" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype1"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 43 20
  subtype2 50 24
  subtype3 30 12
subtype1 subtype2 subtype3 
      63       74       42 
subtype1 subtype2 subtype3 
      20       24       12 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PH 
       40.08         6.74        32.84         8.35         5.59         4.64 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A5 
        8.98        23.01         0.07         0.10         5.19         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A3IK TCGA-DK-A3IL 
       31.40       130.85       112.44        16.14         2.20         3.98 
TCGA-DK-A3IS TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       50.27        17.98        43.59        15.32        26.17         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3N5 TCGA-FD-A3SN 
        0.53         0.56         0.56         1.38        11.93        12.82 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79         1.94        22.98         3.62         5.36        27.45 
TCGA-FD-A62O TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EO 
        4.80        15.16         7.10         4.08         3.22        35.24 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        7.04         0.82         2.86         4.50        15.88        14.07 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.69         3.12         6.38         4.37         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.63         7.79         6.64        19.07         1.51         6.71 
TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        4.27         3.42         3.68 

$subtype2
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.48         6.58        11.93        19.00        12.16 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
        5.06        14.93         5.06         8.25        17.13         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS 
       12.82         2.07         9.99         1.94         2.89         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 
       12.92         5.46         2.53        17.62        10.59         7.76 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
      123.85        87.29         7.82         8.22        10.49        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-FD-A3B3 
        8.28        10.55       140.81        48.00        13.38        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.68         8.94         6.87         4.01        12.43        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       45.93        24.30        16.47         5.49        13.18        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.93        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FT-A61P TCGA-G2-A2EF 
       49.64         2.66         6.25         6.35         6.44        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OS 
       30.61         5.65        26.93        17.72         1.08        20.98 
TCGA-GU-A42Q TCGA-GV-A40E TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        7.63         6.38         3.42         4.64         2.50         6.48 
TCGA-K4-A6FZ TCGA-LC-A66R 
        1.81         6.31 

$subtype3
TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F7 TCGA-CF-A1HR 
        2.66        17.85        19.46        14.89         2.04         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.69         0.13         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        7.20        16.27         1.84        18.41        19.00         8.91 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IT TCGA-DK-A3IV TCGA-E7-A3Y1 TCGA-E7-A5KF 
       15.62         1.81        21.30         9.67         0.10         0.66 
TCGA-E7-A678 TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BY 
        0.82        22.45        46.78        14.89        13.35         6.84 
TCGA-FD-A5C0 TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3I6 
        6.87         3.48        22.32        17.26        20.12         2.24 
TCGA-GC-A3OO TCGA-GD-A3OP TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QI TCGA-K4-A3WS 
       15.81         2.10        11.31         6.41         4.11         8.71 

subtype1 subtype2 subtype3 
    0.07     0.43     0.07 
subtype1 subtype2 subtype3 
  130.85   140.81    46.78 
subtype1 subtype2 subtype3 
   6.640    9.465    7.035 
[1] "0.1 - 130.8 (6.6)" "0.4 - 140.8 (9.5)" "0.1 - 46.8 (7.0)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[139] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[151] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[175] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[139] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[151] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[175] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [49] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
 [73] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[139] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[145] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[151] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[175] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2       22        17       24
  subtype2       0       20        36       18
  subtype3       0       17        12       14
D2V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       24 27  9
  subtype2       17 41 11
  subtype3       12 20  7
D2V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 35  9 13  2
  subtype2 53  7  9  3
  subtype3 26  1 11  1
D2V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 34  2 29
  subtype2 35  1 39
  subtype3 31  2 12
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1 14 52
  subtype2 26 49
  subtype3  7 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   52
  subtype2   26   49
  subtype3    7   38
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       26        7
  MALE         52       49       38
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 25  6
  subtype2 16 11
  subtype3 20 16
  subtype4  2  3
  subtype5 10 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      31       27       36        5       20 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       11       16        3       10 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR 
       40.08        17.85        19.46         4.64        23.01         0.46 
TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AC 
        0.69         5.19        16.27         2.53        19.00       130.85 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3X2 TCGA-E7-A3Y1 
      112.44        15.62        10.59         3.98        17.98         0.10 
TCGA-FD-A3NA TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GD-A2C5 
       45.93         3.48         4.08         0.82         2.86         7.69 
TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       11.31         5.69         7.79         6.64        19.07         1.51 
TCGA-H4-A2HQ 
        6.71 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-C4-A0F0 TCGA-DK-A1AB 
        7.33         6.58         5.06         8.35         1.94         8.91 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A3WY TCGA-FD-A3B3 
       17.62         1.81         2.20        21.30       140.81        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.68         6.87         4.01        12.43        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-GD-A3OP 
       16.47         5.49        46.78        19.79         1.94         2.10 
TCGA-GV-A3JV TCGA-K4-A3WU TCGA-K4-A3WV 
        4.37         3.42         4.64 

$subtype3
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T 
        2.66         6.74        19.00        32.84        12.16        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F1 
       14.93         5.06         8.25        17.13        12.82         2.89 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AE 
        2.04         0.43         5.46         2.14        31.40        16.14 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-E5-A2PC 
        7.76       123.85         8.22        20.02        48.00        43.59 
TCGA-E7-A3X6 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-G2-A2EJ TCGA-G2-A2EO 
       13.38         8.94        11.93        12.82        30.61        35.24 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI TCGA-GV-A40E 
       17.26         2.24        17.72         1.08         4.11         6.38 

$subtype4
TCGA-BT-A0YX TCGA-BT-A2LB TCGA-DK-A3IQ TCGA-G2-A2EK TCGA-GD-A3OQ 
       11.93         5.59        10.49         5.65         3.12 

$subtype5
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IM TCGA-DK-A3IV 
        3.65         2.07         8.98        12.92         7.82         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-G2-A2EC 
        8.28        10.55        15.88        13.18        15.16        22.32 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GD-A3OS TCGA-GV-A3JW 
       61.94        26.93         7.04        20.12        20.98         6.41 
TCGA-GV-A3QF TCGA-K4-A3WS 
        7.63         8.71 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     1.81     0.43     3.12     2.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.85   140.81   123.85    11.93    61.94 
subtype1 subtype2 subtype3 subtype4 subtype5 
    7.69     7.33    12.49     5.65    10.11 
[1] "0.1 - 130.8 (7.7)"  "1.8 - 140.8 (7.3)"  "0.4 - 123.8 (12.5)"
[4] "3.1 - 11.9 (5.7)"   "2.1 - 61.9 (10.1)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype4"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype5" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [49] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3" "subtype4"
 [55] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype5" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype5"
 [85] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype4"
 [91] "subtype5" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[103] "subtype4" "subtype5" "subtype1" "subtype2" "subtype5" "subtype1"
[109] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype4"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype5" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [49] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3" "subtype4"
 [55] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype5" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype5"
 [85] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype4"
 [91] "subtype5" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[103] "subtype4" "subtype5" "subtype1" "subtype2" "subtype5" "subtype1"
[109] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype4"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype4" "subtype5" "subtype1" "subtype3" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
 [31] "subtype1" "subtype5" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [49] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3" "subtype4"
 [55] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype5" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype5"
 [85] "subtype1" "subtype1" "subtype5" "subtype5" "subtype3" "subtype4"
 [91] "subtype5" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[103] "subtype4" "subtype5" "subtype1" "subtype2" "subtype5" "subtype1"
[109] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype1" "subtype5" "subtype2" "subtype2"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       11         9       12
  subtype2       0        5         8       15
  subtype3       0        8        16       11
  subtype4       0        1         3        1
  subtype5       0       10         6        4
D3V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       10 15  4
  subtype2        6 14  8
  subtype3        8 21  5
  subtype4        0  3  1
  subtype5        3  9  1
D3V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 19  1  9  2
  subtype2 13  3  9  2
  subtype3 23  5  4  2
  subtype4  4  1  0  0
  subtype5 11  2  2  0
D3V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 24  2  9
  subtype2 10  2 16
  subtype3 25  0 11
  subtype4  4  0  1
  subtype5  9  1 10
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1  7 29
  subtype2 10 18
  subtype3  8 28
  subtype4  2  3
  subtype5  6 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   29
  subtype2   10   18
  subtype3    8   28
  subtype4    2    3
  subtype5    6   14
D3V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        2       10        1       10 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype5" "subtype5" "subtype1" "subtype3" "subtype5"
[13] "subtype5" "subtype3" "subtype5" "subtype3" "subtype3" "subtype5"
[19] "subtype5" "subtype1" "subtype1" "subtype3" "subtype3" "subtype5"
[25] "subtype5" "subtype1" "subtype5" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype1"
D3V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       17       22        2       13 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype5" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype5" "subtype3" "subtype1" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[25] "subtype1" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype5" "subtype1" "subtype2"
[43] "subtype2" "subtype3" "subtype2" "subtype5" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype5" "subtype3" "subtype5"
[55] "subtype3" "subtype5" "subtype1" "subtype3" "subtype3" "subtype1"
[61] "subtype5" "subtype1" "subtype2" "subtype1" "subtype5" "subtype2"
[67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[73] "subtype1" "subtype5" "subtype2"
D3V10, continuous
D3V11, continuous

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 28  8
  subtype2 12  6
  subtype3 11 12
  subtype4 22 20
subtype1 subtype2 subtype3 subtype4 
      36       18       23       42 
subtype1 subtype2 subtype3 subtype4 
       8        6       12       20 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-C4-A0F1 
       40.08         2.66        11.93        17.85        19.46         2.89 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       23.01         0.46         0.69         5.19        16.27         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 
        2.14        31.40        19.00       112.44        15.62        10.59 
TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SM 
       48.00        13.38         0.10         8.94        45.93        16.47 
TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GD-A3OQ 
        4.08        35.24        20.12         0.82         2.86         3.12 
TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       11.31         5.69         7.79         6.64        19.07         1.51 

$subtype2
TCGA-BT-A3PK TCGA-CU-A0YN TCGA-DK-A3IM TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        2.07        12.92         7.82         9.67         8.28        10.55 
TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       13.18        15.16         3.48        22.32        61.94        30.61 
TCGA-G2-A3IB TCGA-GD-A3OS TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E TCGA-H4-A2HQ 
        7.04        20.98         6.41         7.63         6.38         6.71 

$subtype3
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       19.00        32.84        12.16        14.89        14.93         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-CF-A1HS TCGA-CU-A3KJ 
        8.25        17.13         4.64        12.82         0.43         5.46 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-FD-A3B7 TCGA-FD-A3N6 
      130.85        16.14        17.98        43.59         4.01        15.88 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI 
       26.93        17.26        17.72         1.08         4.11 

$subtype4
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LB 
        7.33         6.74         6.58         5.06         8.35         5.59 
TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F7 TCGA-DK-A1AB TCGA-DK-A1AF 
        3.65         8.98         1.94         2.04         8.91        17.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
        1.81         7.76       123.85         2.20         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 
       10.49        21.30        20.02       140.81        12.89        15.68 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        6.87        12.43        11.93        24.30        22.45        12.82 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-G2-A2EK TCGA-GC-A3I6 
        5.49        46.78        19.79         1.94         5.65         2.24 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        7.69         2.10         4.37         8.71         3.42         4.64 

subtype1 subtype2 subtype3 subtype4 
    0.10     2.07     0.43     1.81 
subtype1 subtype2 subtype3 subtype4 
  112.44    61.94   130.85   140.81 
subtype1 subtype2 subtype3 subtype4 
  10.950    8.975   14.930    7.725 
[1] "0.1 - 112.4 (10.9)" "2.1 - 61.9 (9.0)"   "0.4 - 130.8 (14.9)"
[4] "1.8 - 140.8 (7.7)" 
  [1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [13] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
 [25] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
 [43] "subtype3" "subtype4" "subtype1" "subtype4" "subtype1" "subtype4"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [55] "subtype4" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [67] "subtype4" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
 [73] "subtype3" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
 [79] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
  [1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [13] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
 [25] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
 [43] "subtype3" "subtype4" "subtype1" "subtype4" "subtype1" "subtype4"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [55] "subtype4" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [67] "subtype4" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
 [73] "subtype3" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
 [79] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
  [1] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
  [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [13] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
 [25] "subtype4" "subtype1" "subtype1" "subtype4" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype4" "subtype3" "subtype1"
 [43] "subtype3" "subtype4" "subtype1" "subtype4" "subtype1" "subtype4"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [55] "subtype4" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype4"
 [67] "subtype4" "subtype1" "subtype4" "subtype3" "subtype4" "subtype4"
 [73] "subtype3" "subtype1" "subtype4" "subtype4" "subtype1" "subtype4"
 [79] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype1" "subtype2" "subtype1" "subtype4" "subtype2" "subtype1"
[109] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
[115] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       14        12       11
  subtype2       0        9         5        4
  subtype3       0        4        11        7
  subtype4       0        8        14       21
D4V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       14 15  6
  subtype2        2  6  1
  subtype3        3 17  2
  subtype4        8 24 10
D4V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 23  4  7  1
  subtype2  9  0  2  1
  subtype3 15  3  4  1
  subtype4 23  5 11  3
D4V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 29  1 10
  subtype2  8  2  8
  subtype3 13  0 10
  subtype4 22  2 19
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1  6 35
  subtype2  5 13
  subtype3  6 17
  subtype4 16 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   35
  subtype2    5   13
  subtype3    6   17
  subtype4   16   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        5        6       16
  MALE         35       13       17       27
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        2        7       11 
 [1] "subtype3" "subtype3" "subtype4" "subtype3" "subtype3" "subtype1"
 [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[13] "subtype1" "subtype4" "subtype4" "subtype4" "subtype1" "subtype3"
[19] "subtype4" "subtype4" "subtype4"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 18  8
  subtype2 37 19
  subtype3 23 14
  subtype4 45 15
subtype1 subtype2 subtype3 subtype4 
      26       56       37       60 
subtype1 subtype2 subtype3 subtype4 
       8       19       14       15 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         6.74         6.48         6.58        19.00 
TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-DK-A1AC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-FD-A3SJ 
       17.13         8.98       130.85        26.17         0.49        24.30 
TCGA-FD-A43P TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3VY TCGA-GC-A3RB 
       14.89        15.16         4.08        26.93         0.82         4.50 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       20.98         6.38         6.15         5.69         7.79         4.11 
TCGA-H4-A2HQ TCGA-K4-A3WV 
        6.71         4.64 

$subtype2
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
        2.66        11.93        32.84        14.93         5.06         8.25 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 
       12.82         2.07         9.99         1.94         2.89         2.04 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 
        0.43        12.92         5.46         8.91        16.14         7.76 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-E5-A2PC 
       87.29         7.82         8.28        10.55        17.98        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        13.38        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS 
        4.01        11.93        15.88        12.82         5.49         1.94 
TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62S TCGA-G2-A2EF 
       12.13         6.87         6.84        49.64         6.35        61.94 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC 
       30.61        17.26         7.04         2.24        15.88        17.72 
TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC 
        1.08         3.12         7.63         6.38         2.50         6.48 
TCGA-K4-A6FZ TCGA-LC-A66R 
        1.81         6.31 

$subtype3
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LB TCGA-BT-A2LD TCGA-DK-A1A3 
       12.16        19.46         5.06         5.59         3.65         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN 
        2.14        17.62         1.81        10.59       123.85         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B8 TCGA-FD-A3SL 
       10.49        21.30        20.02       140.81        12.43        22.45 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43U 
       16.47        13.18        46.78        19.79        14.96        14.93 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       13.35        37.15        11.01         5.69        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FT-A61P TCGA-G2-A2EO TCGA-GC-A3OO TCGA-K4-A3WS 
        2.66         6.25         6.44        35.24        15.81         8.71 
TCGA-K4-A3WU 
        3.42 

$subtype4
TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.85        14.89         8.35         4.64        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         4.90         7.20         5.19        16.27         1.84 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A3IK 
       31.40        18.41        19.00       112.44        15.62         2.20 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
        3.98        50.27         9.67        48.00         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3NA 
        0.56         0.56         0.66         1.38         0.82        45.93 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       22.98         3.62         5.36         4.80         7.10         3.48 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3RD 
        3.22        22.32         5.65        20.12         2.86        14.07 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
        7.69         2.10        11.31         4.37         6.41         7.63 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        6.64        19.07         1.51         4.27         3.42         3.68 

subtype1 subtype2 subtype3 subtype4 
    0.49     0.43     1.81     0.07 
subtype1 subtype2 subtype3 subtype4 
  130.85    87.29   140.81   112.44 
subtype1 subtype2 subtype3 subtype4 
   7.035    8.265   12.430    4.850 
[1] "0.5 - 130.8 (7.0)"  "0.4 - 87.3 (8.3)"   "1.8 - 140.8 (12.4)"
[4] "0.1 - 112.4 (4.8)" 
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
 [13] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype2"
 [19] "subtype1" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
 [31] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype3"
 [67] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype2"
 [73] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [97] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype1"
[109] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[127] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[139] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype2"
[145] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[151] "subtype4" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[157] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
[163] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
[169] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[175] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
 [13] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype2"
 [19] "subtype1" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
 [31] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype3"
 [67] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype2"
 [73] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [97] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype1"
[109] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[127] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[139] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype2"
[145] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[151] "subtype4" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[157] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
[163] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
[169] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[175] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
  [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
 [13] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype2"
 [19] "subtype1" "subtype3" "subtype3" "subtype4" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
 [31] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
 [37] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [43] "subtype2" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
 [49] "subtype4" "subtype4" "subtype4" "subtype2" "subtype1" "subtype4"
 [55] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
 [61] "subtype3" "subtype2" "subtype4" "subtype4" "subtype2" "subtype3"
 [67] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype2"
 [73] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [97] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype1"
[109] "subtype3" "subtype3" "subtype4" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[127] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype3"
[139] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype2"
[145] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[151] "subtype4" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[157] "subtype4" "subtype4" "subtype4" "subtype1" "subtype1" "subtype4"
[163] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype4"
[169] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[175] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        9        10        6
  subtype2       0       14        24       17
  subtype3       0        7        15       16
  subtype4       1       29        16       17
D5V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1        7  9  4
  subtype2       12 28 12
  subtype3        7 26  5
  subtype4       27 25  6
D5V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 15  2  2  1
  subtype2 36  6  7  3
  subtype3 22  4 11  1
  subtype4 41  5 13  1
D5V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 11  2 12
  subtype2 28  0 28
  subtype3 17  2 19
  subtype4 44  1 21
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1  6 20
  subtype2 18 38
  subtype3  9 29
  subtype4 14 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   20
  subtype2   18   38
  subtype3    9   29
  subtype4   14   52
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       18        9       14
  MALE         20       38       29       52
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 54 16
  subtype2 20 12
  subtype3 49 28
subtype1 subtype2 subtype3 
      70       32       77 
subtype1 subtype2 subtype3 
      16       12       28 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20W 
       40.08         2.66        32.84        17.85        14.89         8.35 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S 
       17.13         4.64         8.98        23.01         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR 
        0.07         0.10         0.07         0.10         0.10         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19        16.27         1.84        31.40        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 
      130.85        15.62         2.20        50.27         9.67        48.00 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17         0.10         0.49         0.53         0.56         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X 
        0.66         1.38         0.82        22.98        14.89         3.62 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        5.36         4.80        15.16         7.10         3.48         4.08 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD 
       26.93        20.12         0.82         2.86         4.50        14.07 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.38        11.31         4.37         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         7.79         4.11         6.64        19.07         1.51 
TCGA-H4-A2HQ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        6.71         4.27         3.42         3.68 

$subtype2
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CU-A0YO TCGA-DK-A1A3 
       19.46         5.06         5.59         0.46         4.90         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IL 
        2.14       112.44        17.62         1.81        10.59         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
       10.49        21.30        24.30        22.45        16.47        46.78 
TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.79        14.96        14.93        13.35        27.45         6.87 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GD-A2C5 TCGA-GD-A3OP 
       22.32         5.65        35.24        15.81         7.69         2.10 
TCGA-K4-A3WS TCGA-K4-A3WU 
        8.71         3.42 

$subtype3
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74         6.48         6.58        11.93        19.00 
TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ 
       12.16        14.93         5.06         8.25         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS 
        2.07         9.99         1.94         2.89         2.04         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 
       12.92         5.46         8.91        16.14         7.76       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
       87.29         7.82         8.22        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-FD-A3B3 
      140.81        17.98        43.59        15.32        13.38        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS 
       15.88        45.93        12.82         5.49        13.18         1.94 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       12.13        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FT-A3EE TCGA-FT-A61P 
       49.64         2.66         6.25         6.35         3.22         6.44 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC 
       61.94        30.61        17.26         7.04         2.24        15.88 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E 
       17.72         1.08         3.12        20.98         7.63         6.38 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R 
        4.64         2.50         6.48         1.81         6.31 

subtype1 subtype2 subtype3 
    0.07     0.46     0.43 
subtype1 subtype2 subtype3 
  130.85   112.44   140.81 
subtype1 subtype2 subtype3 
    5.92    11.97     8.25 
[1] "0.1 - 130.8 (5.9)"  "0.5 - 112.4 (12.0)" "0.4 - 140.8 (8.2)" 
  [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [13] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[139] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
  [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [13] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[139] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
  [1] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [13] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[121] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[127] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[139] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[145] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2       32        22       18
  subtype2       0        6         7       18
  subtype3       0       21        36       20
D6V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       30 28  7
  subtype2        5 20  5
  subtype3       18 40 15
D6V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 46  7 10  2
  subtype2 14  2 16  0
  subtype3 54  8  7  4
D6V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 49  3 23
  subtype2 17  2 13
  subtype3 34  0 44
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1 11 65
  subtype2 11 21
  subtype3 25 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   65
  subtype2   11   21
  subtype3   25   53
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11       11       25
  MALE         65       21       53
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 28 11
  subtype2 55 23
  subtype3 39 22
subtype1 subtype2 subtype3 
      39       78       61 
subtype1 subtype2 subtype3 
      11       23       22 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK 
       40.08         2.66        11.93         8.35         3.65         2.07 
TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
        2.89         0.13         7.20         5.19         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IT TCGA-E7-A677 TCGA-FD-A3B7 
      130.85        87.29         2.20        21.30         1.38         4.01 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       12.82         1.94        22.98         6.87        49.64         4.80 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JV 
       15.16         4.08         0.82         1.08         6.38         4.37 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A4AB 
        7.63        19.07         1.51         6.71         3.42         2.50 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V 
        4.27         6.31         3.68 

$subtype2
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A3PH TCGA-BT-A3PJ 
        7.33         6.74        32.84        17.85         4.64        12.82 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T 
        9.99         8.98        23.01         2.04         0.69         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ 
        0.10         0.07         0.10         0.10        12.92         5.46 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I2 
       16.27        31.40        18.41        19.00        15.62         7.76 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 
        7.82        50.27         9.67         8.28        10.55        48.00 
TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ 
       17.98        43.59        15.32        26.17        13.38         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3B5 
        0.53         0.56         0.56         0.66         0.82         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A43P 
        6.87        11.93        15.88        45.93         5.49        14.89 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
       14.93         3.62         5.36         7.10         3.48         3.22 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         2.86         2.24         4.50        15.88        14.07 
TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        3.12         7.63        11.31         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A6FZ TCGA-LT-A5Z6 
        7.79         4.11         6.64         6.38         1.81         3.42 

$subtype3
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
        6.58        19.00        12.16        19.46         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-C4-A0F0 
       14.93         5.06         8.25        17.13         5.59         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD 
        0.46         0.43         4.90         2.53         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
       16.14        17.62         1.81        10.59       123.85         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WY TCGA-E7-A3Y1 TCGA-FD-A3B3 
        8.22        10.49        20.02       140.81         0.10        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP 
       15.68        12.43        24.30        22.45        16.47        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        14.96        12.13        13.35        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       11.01         6.87         5.69         6.84        27.45         2.66 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO 
        6.25         6.35         6.44        22.32         5.65        15.81 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-K4-A3WS TCGA-K4-A3WV 
       17.72         7.69         2.10        20.98         8.71         4.64 
TCGA-K4-A4AC 
        6.48 

subtype1 subtype2 subtype3 
    0.13     0.07     0.10 
subtype1 subtype2 subtype3 
  130.85    61.94   140.81 
subtype1 subtype2 subtype3 
   4.370    7.775   11.010 
[1] "0.1 - 130.8 (4.4)"  "0.1 - 61.9 (7.8)"   "0.1 - 140.8 (11.0)"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[151] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[157] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[163] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[175] "subtype1" "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[151] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[157] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[163] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[175] "subtype1" "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [67] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
 [91] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[109] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[121] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[127] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[151] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[157] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[163] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[175] "subtype1" "subtype1" "subtype2" "subtype1"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        8        15       18
  subtype2       1       36        27       16
  subtype3       0       15        22       22
D7V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       12 20  8
  subtype2       29 33  8
  subtype3       12 35 10
D7V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 22  7  9  2
  subtype2 53  6  7  4
  subtype3 38  4 17  0
D7V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 21  1 20
  subtype2 51  2 28
  subtype3 28  2 31
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1  4 39
  subtype2 18 63
  subtype3 24 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   39
  subtype2   18   63
  subtype3   24   37
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       18       24
  MALE         39       63       37
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 86 35
  subtype2 10  7
  subtype3 26 14
subtype1 subtype2 subtype3 
     121       17       40 
subtype1 subtype2 subtype3 
      35        7       14 
$subtype1
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        7.33         6.74         6.58        19.00        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.85        19.46        14.89        14.93         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.13         5.59        12.82         8.98         1.94        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        2.04         0.46         0.43         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
        0.07         0.10         0.10        12.92         4.90         5.46 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
       16.27        31.40        18.41        19.00         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM 
       16.14        17.62        15.62         7.76       123.85         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        50.27         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       48.00        17.98        43.59        15.32        26.17        13.38 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.56         0.56         0.66 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
        0.82        12.89        15.68         8.94         6.87        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45        16.47 
TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       13.18        14.89        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.35        37.15         6.87         5.36         5.69         6.84 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        2.66         6.25         6.35         7.10         3.48         3.22 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.44        61.94        30.61         5.65        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         7.04        20.12         2.86         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ 
        4.50        15.88        14.07        17.72         7.69         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
       20.98         7.63        11.31         6.41         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ 
        4.11         6.64         6.38         4.64         6.48         1.81 
TCGA-LT-A5Z6 
        3.42 

$subtype2
TCGA-BT-A20R TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK 
        5.06         2.53         2.14         1.81        10.59         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-FD-A3SQ TCGA-FD-A3SR 
        3.98        10.49        21.30        20.02        46.78        19.79 
TCGA-FD-A5C0 TCGA-G2-A2EC TCGA-GD-A3OP TCGA-K4-A3WS TCGA-K4-A4AB 
        6.87        22.32         2.10         8.71         2.50 

$subtype3
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH 
       40.08         2.66        11.93         8.35         3.65         4.64 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU 
        2.07         9.99         2.89         0.13         7.20         5.19 
TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-E7-A677 TCGA-FD-A3B7 TCGA-FD-A3SN 
        1.84       130.85        87.29         1.38         4.01        12.82 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C1 
        5.49         1.94        22.98        11.01        27.45        49.64 
TCGA-FD-A62O TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P 
        4.80        15.16         4.08         0.82         1.08         6.38 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.37         6.15         7.63        19.07         1.51         6.71 
TCGA-K4-A3WU TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V 
        3.42         4.27         6.31         3.68 

subtype1 subtype2 subtype3 
    0.07     1.81     0.13 
subtype1 subtype2 subtype3 
  140.81    46.78   130.85 
subtype1 subtype2 subtype3 
    8.91     6.87     5.34 
[1] "0.1 - 140.8 (8.9)" "1.8 - 46.8 (6.9)"  "0.1 - 130.8 (5.3)"
  [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[151] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[151] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype3" "subtype3" "subtype1" "subtype3"
  [1] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [43] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[151] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[157] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[169] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype3" "subtype3" "subtype1" "subtype3"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       48        44       28
  subtype2       0        4         4        9
  subtype3       1        7        16       19
D8V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       39 55 16
  subtype2        3 10  3
  subtype3       11 23  7
D8V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 83  7 17  4
  subtype2  8  1  8  0
  subtype3 22  9  8  2
D8V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 70  4 50
  subtype2 11  0  6
  subtype3 19  1 23
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1 35 89
  subtype2  6 11
  subtype3  5 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   89
  subtype2    6   11
  subtype3    5   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35        6        5
  MALE         89       11       39
D8V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
      39        2        9 
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
D8V9, continuous
D8V10, continuous
D8V11, continuous

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 18  9
  subtype2 30 20
  subtype3 43 11
  subtype4 31 16
subtype1 subtype2 subtype3 subtype4 
      27       50       54       47 
subtype1 subtype2 subtype3 subtype4 
       9       20       11       16 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 
       40.08         2.66        11.93         8.35         3.65         2.89 
TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 
        0.13         7.20         1.84         2.14       130.85        87.29 
TCGA-DK-A3IK TCGA-E7-A677 TCGA-FD-A3SS TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        2.20         1.38         1.94         6.87        49.64         4.80 
TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO 
       15.16         6.38         4.37         7.63        19.07         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A4AB 
        6.71         3.42         2.50 

$subtype2
TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V 
        7.33        19.00        32.84        12.16        14.93         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 
        8.25        17.13        12.82         2.07         9.99         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IM 
        0.43        12.92         5.46        16.14         7.76         7.82 
TCGA-DK-A3IN TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ 
        8.22         8.28        10.55        17.98        43.59        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
       12.89        15.68         8.94         6.87         4.01        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       15.88         5.49        12.13         3.22        61.94        30.61 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3YS 
       17.26         7.04         2.24         4.50        15.88         1.08 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E TCGA-K4-A3WV TCGA-K4-A4AC 
        3.12        20.98         7.63         6.38         4.64         6.48 
TCGA-K4-A6FZ TCGA-LC-A66R 
        1.81         6.31 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20P TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 
        6.74        17.85         4.64         8.98        23.01         2.04 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG 
        5.19        16.27        31.40        18.41        19.00        15.62 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       50.27         9.67        48.00        26.17        13.38         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        0.49         0.53         0.56         0.56         0.66         0.82 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BV 
       45.93        16.47        22.98        14.89         3.62         5.36 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY 
        7.10         3.48         4.08        26.93        20.12         0.82 
TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.86        14.07        11.31         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V 
        7.79         4.11         6.64         4.27         3.42         3.68 

$subtype4
TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A2LB TCGA-CF-A1HR 
        6.58        19.46         5.06        14.89         5.59         0.46 
TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        4.90         2.53         8.91       112.44        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       10.59       123.85         3.98        10.49        21.30        20.02 
TCGA-DK-A3WY TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SP 
      140.81        12.43        24.30        22.45        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        14.96        14.93        13.35        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       11.01         6.87         5.69         6.84        27.45         2.66 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO 
        6.25         6.35         6.44        22.32         5.65        35.24 
TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-K4-A3WS 
       15.81        17.72         7.69         2.10         8.71 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.43     0.07     0.46 
subtype1 subtype2 subtype3 subtype4 
  130.85    61.94    50.27   140.81 
subtype1 subtype2 subtype3 subtype4 
   4.800    8.265    5.920   12.430 
[1] "0.1 - 130.8 (4.8)"  "0.4 - 61.9 (8.3)"   "0.1 - 50.3 (5.9)"  
[4] "0.5 - 140.8 (12.4)"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype4" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [61] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [67] "subtype3" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [73] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype3"
 [97] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[103] "subtype4" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
[109] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[115] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype1"
[121] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype4"
[133] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype2"
[139] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype4"
[145] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
[151] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[157] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype4" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[175] "subtype3" "subtype2" "subtype3" "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype4" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [61] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [67] "subtype3" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [73] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype3"
 [97] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[103] "subtype4" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
[109] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[115] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype1"
[121] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype4"
[133] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype2"
[139] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype4"
[145] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
[151] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[157] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype4" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[175] "subtype3" "subtype2" "subtype3" "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype4" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype1" "subtype4" "subtype1" "subtype3"
 [49] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [61] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype4"
 [67] "subtype3" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
 [73] "subtype4" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype3"
 [97] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype4"
[103] "subtype4" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
[109] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[115] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype1"
[121] "subtype1" "subtype4" "subtype1" "subtype4" "subtype4" "subtype1"
[127] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype4"
[133] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype2"
[139] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype4"
[145] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
[151] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[157] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[163] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype4" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[175] "subtype3" "subtype2" "subtype3" "subtype3"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        6         9       13
  subtype2       0       15        23       11
  subtype3       1       29        16       11
  subtype4       0        9        16       21
D9V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1       10 12  7
  subtype2       11 25  9
  subtype3       24 20  4
  subtype4        8 31  6
D9V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 14  4  8  2
  subtype2 35  5  5  2
  subtype3 37  4  5  2
  subtype4 27  4 15  0
D9V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 16  1 13
  subtype2 25  0 25
  subtype3 38  3 16
  subtype4 21  1 25
D9V6, multiclass
D9V7, binary
          cls
clus        0  1
  subtype1  4 26
  subtype2 15 35
  subtype3 10 48
  subtype4 17 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   26
  subtype2   15   35
  subtype3   10   48
  subtype4   17   30
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       15       10       17
  MALE         26       35       48       30
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 32 18
  subtype2 39 16
  subtype3 32 13
  subtype4 19  9
subtype1 subtype2 subtype3 subtype4 
      50       55       45       28 
subtype1 subtype2 subtype3 subtype4 
      18       16       13        9 
$subtype1
TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
        6.58        17.85        19.46         5.06        14.89        14.93 
TCGA-BT-A2LB TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 
        5.59         2.04         0.46         4.90        16.27         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX 
        2.14         8.91       112.44        16.14        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT 
       10.59       123.85         2.20         3.98        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       20.02       140.81        12.89        12.43        24.30        22.45 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A5BR TCGA-FD-A5BT 
       13.18        46.78        19.79        14.96        13.35        11.01 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FT-A61P 
        6.87         6.84         6.87         6.25         6.35         6.44 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP 
       22.32         5.65        15.81        17.72         7.69         2.10 
TCGA-K4-A3WS TCGA-K4-A4AB 
        8.71         2.50 

$subtype2
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 
        6.74        32.84         5.06         4.64         8.98        23.01 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IN 
       12.92        31.40        18.41        19.00        15.62         8.22 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ 
       50.27         9.67        48.00        17.98        43.59        15.32 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17         0.10         0.49         0.53         0.56         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43N TCGA-FD-A43P 
        0.66         0.82        45.93        16.47        22.98        14.89 
TCGA-FD-A43X TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EL 
        3.62         5.36         7.10         3.48         3.22        26.93 
TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GU-A42R 
       20.12         2.86         4.50        14.07         3.12        11.31 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-K4-A3WV 
        6.41         5.69         7.79         4.11         6.64         4.64 
TCGA-LT-A5Z6 
        3.42 

$subtype3
TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ 
        7.33        19.00        12.16         8.25        17.13        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A2I2 
        2.07         9.99         1.94         0.43         5.46         7.76 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-E7-A3X6 TCGA-FD-A3B4 
       87.29         7.82         8.28        10.55        13.38        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN 
        8.94         6.87         4.01        11.93        15.88        12.82 
TCGA-FD-A3SO TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C1 
        5.49        14.93        12.13        37.15         5.69        49.64 
TCGA-FD-A62N TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        2.66        61.94        30.61        35.24        17.26         7.04 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E 
        2.24        15.88         1.08        20.98         7.63         6.38 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R 
        6.48         1.81         6.31 

$subtype4
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 
       40.08         2.66        11.93         8.35         3.65         2.89 
TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-E7-A677 
        0.13         7.20         5.19         1.84       130.85         1.38 
TCGA-FD-A3SS TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
        1.94        27.45         4.80        15.16         4.08         0.82 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO 
        6.38         4.37         6.15         7.63        19.07         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A6MB TCGA-MV-A51V 
        6.71         3.42         4.27         3.68 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.07     0.43     0.13 
subtype1 subtype2 subtype3 subtype4 
  140.81    50.27    87.29   130.85 
subtype1 subtype2 subtype3 subtype4 
  10.800    6.640    8.940    4.585 
[1] "0.5 - 140.8 (10.8)" "0.1 - 50.3 (6.6)"   "0.4 - 87.3 (8.9)"  
[4] "0.1 - 130.8 (4.6)" 
  [1] "subtype4" "subtype3" "subtype4" "subtype2" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype4" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype4" "subtype1"
[121] "subtype3" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
[127] "subtype2" "subtype2" "subtype4" "subtype2" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype1"
[145] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[151] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[157] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype2"
[163] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
[169] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
[175] "subtype4" "subtype3" "subtype2" "subtype4"
  [1] "subtype4" "subtype3" "subtype4" "subtype2" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype4" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype4" "subtype1"
[121] "subtype3" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
[127] "subtype2" "subtype2" "subtype4" "subtype2" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype1"
[145] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[151] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[157] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype2"
[163] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
[169] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
[175] "subtype4" "subtype3" "subtype2" "subtype4"
  [1] "subtype4" "subtype3" "subtype4" "subtype2" "subtype1" "subtype4"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype2" "subtype4" "subtype3" "subtype3"
 [19] "subtype1" "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype4" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype4" "subtype2" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
 [43] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
[103] "subtype1" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[115] "subtype1" "subtype2" "subtype3" "subtype1" "subtype4" "subtype1"
[121] "subtype3" "subtype3" "subtype4" "subtype1" "subtype1" "subtype4"
[127] "subtype2" "subtype2" "subtype4" "subtype2" "subtype1" "subtype1"
[133] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype1"
[145] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[151] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
[157] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype2"
[163] "subtype2" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
[169] "subtype1" "subtype4" "subtype2" "subtype1" "subtype3" "subtype3"
[175] "subtype4" "subtype3" "subtype2" "subtype4"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       10        19       20
  subtype2       1       28        16       13
  subtype3       0       15        19       10
  subtype4       1        6        10       13
D10V3, multiclass
          vv
clus       T0+T1+T2 T3 T4
  subtype1        9 31  8
  subtype2       24 20  7
  subtype3       11 24  5
  subtype4        9 13  6
D10V4, multiclass
          vv
clus       N0 N1 N2 N3
  subtype1 30  2 17  0
  subtype2 38  4  7  2
  subtype3 31  5  3  2
  subtype4 14  6  6  2
D10V5, multiclass
          vv
clus       M0 M1 MX
  subtype1 27  1 22
  subtype2 36  3 20
  subtype3 21  0 24
  subtype4 16  1 13
D10V6, multiclass
D10V7, binary
          cls
clus        0  1
  subtype1 19 31
  subtype2 13 46
  subtype3 10 35
  subtype4  4 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   31
  subtype2   13   46
  subtype3   10   35
  subtype4    4   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       13       10        4
  MALE         31       46       35       27
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
> q(save="no")
