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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/BLCA-TP/3143259/1.GDAC_mergedClustering.Finished/BLCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/3132613/1.GDAC_clinicalDataPicker.Finished/BLCA-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=135, in cluster file=153, common to both=134
[1]   8 134
[1] "CN_CNMF"
[1] 3
 1  2  3 
39 58 34 
 1  2  3 
39 58 34 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
34 46 33 21 
 1  2  3  4 
34 46 33 21 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
12 10 14 17 
 1  2  3  4 
12 10 14 17 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
14 15 24 
 1  2  3 
14 15 24 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
45 21 41 24 
 1  2  3  4 
45 21 41 24 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
29 45 57 
 1  2  3 
29 45 57 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
32 54 48 
 1  2  3 
32 54 48 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
20 63  7 36  8 
 1  2  3  4  5 
20 63  7 36  8 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "TOBACCOSMOKINGHISTORYINDICATOR"        
[15] "DISTANT.METASTASIS"                    
[16] "LYMPH.NODE.METASTASIS"                 
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 134 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
         389           NA           NA           NA           NA          363 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
          NA           NA           NA           NA           NA          179 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
         111           NA           NA           59           88           61 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
          NA           14           13           21           NA           NA 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
          NA           NA           NA           NA          219          166 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
         158          246           77           NA          955          273 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
         214          271         3616         3056          218          178 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
         202           55          322           NA         3767         2291 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
          67          121          238           NA          319         1151 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
         168          350           NA          252           NA         3989 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1108           NA            3          268          253           NA 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
         209           NA          336          272          242          974 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
          NA          334          186          207           NA          138 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FJ-A3Z7 
          NA           NA           59          240          208          461 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
         124           71          417         1518          806          172 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
          NA          997          525          214           NA           25 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
          87           68           40          137           42           31 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
          76           33          234           64           95          177 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
         194          230           98          133          195          187 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
         173          232           NA          237          125          202 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
         194          162           46          204           NA          265 
TCGA-K4-A3WU TCGA-K4-A3WV 
         104          141 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=91,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                            "GENDER"                        
 [3] "KARNOFSKY.PERFORMANCE.SCORE"    "NUMBERPACKYEARSSMOKED"         
 [5] "TOBACCOSMOKINGHISTORYINDICATOR" "DISTANT.METASTASIS"            
 [7] "LYMPH.NODE.METASTASIS"          "NUMBER.OF.LYMPH.NODES"         
 [9] "TUMOR.STAGECODE"                "NEOPLASM.DISEASESTAGE"         
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T2 T2A T2B  T3 T3A T3B  T4 T4A 
  5   3  14  12  12  11   1  13 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 134 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=43, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=36, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=5, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=13, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 27 10
  subtype2 41 13
  subtype3 24  9
subtype1 subtype2 subtype3 
      37       54       33 
subtype1 subtype2 subtype3 
      10       13        9 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LD 
       12.79         2.66        26.10        14.89         5.06         3.65 
TCGA-BT-A3PH TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        4.64         7.20         5.46         2.14        31.40         8.98 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-E5-A2PC 
      100.47        10.59        75.32         2.20         7.82        36.43 
TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-A3VY 
        8.94        24.30        19.79         2.33        20.12         0.82 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        4.50         1.02         5.82         3.22         4.37         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HQ 
        5.69         7.63         7.79         4.11         6.38         6.71 
TCGA-K4-A3WV 
        4.64 

$subtype2
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74         6.58        11.93        19.00        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.85        19.46         8.61         8.25         1.94         2.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AA 
        0.46         0.69         4.90         8.09         2.53         7.04 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS 
        8.91         7.17         5.85         6.64        10.49        37.84 
TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E7-A3Y1 TCGA-FD-A3B4 
        5.52         8.28        10.55       131.15         0.10         8.32 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        11.05         7.96        32.02         6.12         6.81 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43U TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        4.54        46.78         6.84        26.50         5.65        32.78 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GD-A3OP 
       17.26         7.04         2.86         2.24         2.50         2.10 
TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU 
        3.12         7.56         6.64         1.51         8.71         3.42 

$subtype3
TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A0YN 
        5.06         8.35         5.88         8.98         0.43        12.92 
TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
        5.19       118.88         1.81         7.76       123.85         3.98 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 
        8.22        11.51         9.67         8.81         6.87         8.94 
TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       10.98         5.49         1.94         7.89        15.16         4.08 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 
       49.91        26.93         1.32         1.38         1.08         7.69 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A40G 
        6.38         6.15         5.33 

subtype1 subtype2 subtype3 
    0.82     0.10     0.43 
subtype1 subtype2 subtype3 
  100.47   131.15   123.85 
subtype1 subtype2 subtype3 
    6.41     7.04     7.69 
[1] "0.8 - 100.5 (6.4)" "0.1 - 131.2 (7.0)" "0.4 - 123.8 (7.7)"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [25] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [49] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [91] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [97] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[121] "subtype1" "subtype2" "subtype2" "subtype1"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 10 29
  subtype2 15 43
  subtype3  8 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   29
  subtype2   15   43
  subtype3    8   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       15        8
  MALE         29       43       26
D1V4, continuous
D1V5, continuous
D1V6, continuous
          vv
clus       M0 M1 MX
  subtype1  7  0 18
  subtype2 17  1 15
  subtype3 10  1 11
D1V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1  8  4  6  1  5
  subtype2 25  1  5  0  2
  subtype3 12  4  3  2  1
D1V8, multiclass
D1V9, continuous
D1V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1        9         6       10
  subtype2       10        15        7
  subtype3        7         6        9
D1V11, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 27  6
  subtype2 30 15
  subtype3 23  5
  subtype4 14  7
subtype1 subtype2 subtype3 subtype4 
      33       45       28       21 
subtype1 subtype2 subtype3 subtype4 
       6       15        5        7 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-C4-A0EZ 
       12.79         5.06         8.35         5.88         3.65         8.98 
TCGA-C4-A0F6 TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        2.01         5.19         2.53         8.98       118.88       100.47 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR 
       10.59         2.20         3.98        32.02        24.30        19.79 
TCGA-FD-A43N TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY 
        7.89        15.16         4.08         5.65        20.12         0.82 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.50         1.02         7.69         6.38         5.69         7.63 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         1.51         6.71 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20U 
        7.33         6.58        11.93        19.00        12.16         8.61 
TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-CU-A0YN 
        5.06         8.25         1.94         2.89         0.43        12.92 
TCGA-CU-A3KJ TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
        5.46         7.17         5.85         7.76       123.85        75.32 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        7.82         8.22        11.51         8.28        10.55       131.15 
TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       36.43         8.81         8.32         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43U TCGA-G2-A2EF 
       11.05         6.12         5.49         4.54         6.84        49.91 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GU-A42Q 
       26.50        26.93         2.50         1.08         5.82         7.56 
TCGA-GV-A40E TCGA-K4-A3WU TCGA-K4-A3WV 
        6.38         3.42         4.64 

$subtype3
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A3PH TCGA-CF-A27C TCGA-CU-A3YL 
        2.66         6.74        26.10         4.64         0.69         8.09 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IS TCGA-FD-A3N5 
        2.14        31.40         7.04         6.64        37.84         8.94 
TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A2ES 
        7.96         6.81         1.94         2.33        32.78        17.26 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A3OQ TCGA-GV-A3JV 
        7.04         2.86         2.24         1.38         3.12         4.37 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        6.15         4.11         6.64         5.33 

$subtype4
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CU-A0YO 
       17.85        19.46        14.89         2.04         0.46         4.90 
TCGA-CU-A0YR TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
        7.20         8.91         1.81        10.49         5.52         9.67 
TCGA-E7-A3Y1 TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-G2-A2EC TCGA-GC-A3OO TCGA-GD-A3OP 
        0.10        10.98        46.78        13.71         1.32         2.10 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-K4-A3WS 
        3.22         6.41         8.71 

subtype1 subtype2 subtype3 subtype4 
    0.82     0.43     0.69     0.10 
subtype1 subtype2 subtype3 subtype4 
  118.88   131.15    37.84    46.78 
subtype1 subtype2 subtype3 subtype4 
   6.710    7.760    6.395    7.200 
[1] "0.8 - 118.9 (6.7)" "0.4 - 131.2 (7.8)" "0.7 - 37.8 (6.4)" 
[4] "0.1 - 46.8 (7.2)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype4" "subtype4" "subtype1"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [25] "subtype4" "subtype4" "subtype2" "subtype3" "subtype2" "subtype4"
 [31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype4" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype3" "subtype4" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype1" "subtype4" "subtype2" "subtype3" "subtype2"
 [79] "subtype2" "subtype4" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype4" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype4" "subtype4" "subtype1"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [25] "subtype4" "subtype4" "subtype2" "subtype3" "subtype2" "subtype4"
 [31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype4" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype3" "subtype4" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype1" "subtype4" "subtype2" "subtype3" "subtype2"
 [79] "subtype2" "subtype4" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype4" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype2" "subtype4" "subtype4" "subtype1"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [19] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [25] "subtype4" "subtype4" "subtype2" "subtype3" "subtype2" "subtype4"
 [31] "subtype4" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype1" "subtype3" "subtype4" "subtype1" "subtype1"
 [43] "subtype2" "subtype2" "subtype3" "subtype4" "subtype1" "subtype2"
 [49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [61] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [73] "subtype1" "subtype1" "subtype4" "subtype2" "subtype3" "subtype2"
 [79] "subtype2" "subtype4" "subtype1" "subtype3" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype3" "subtype4" "subtype2" "subtype2"
 [91] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype3" "subtype4" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype1" "subtype4" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[121] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype2"
[127] "subtype2"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 10 24
  subtype2 16 30
  subtype3  3 30
  subtype4  5 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   24
  subtype2   16   30
  subtype3    3   30
  subtype4    5   16
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10       16        3        5
  MALE         24       30       30       16
D2V4, continuous
D2V5, continuous
D2V6, continuous
          vv
clus       M0 M1 MX
  subtype1  8  0 10
  subtype2  9  1 17
  subtype3 12  0 12
  subtype4  5  1  5
D2V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1  5  3  7  1  2
  subtype2 18  4  2  1  2
  subtype3 17  2  2  1  2
  subtype4  5  0  3  0  2
D2V8, multiclass
D2V9, continuous
D2V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1        4         4       10
  subtype2        6        13        7
  subtype3       11         7        6
  subtype4        5         3        3
D2V11, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  8  4
  subtype2  5  5
  subtype3 11  2
  subtype4  8  9
subtype1 subtype2 subtype3 subtype4 
      12       10       13       17 
subtype1 subtype2 subtype3 subtype4 
       4        5        2        9 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.79         6.58         8.98        12.92         8.81         8.32 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-H4-A2HQ 
       13.71        49.91        26.50         5.65        26.93         6.71 

$subtype2
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-C4-A0F0 
        7.33         2.66         5.06         8.61         8.35         1.94 
TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        2.53       100.47         5.85         1.81 

$subtype3
TCGA-BT-A0YX TCGA-BT-A20Q TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       11.93        19.46         2.89         2.01         0.46         0.69 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-GD-A2C5 
        2.14         7.04         8.91         6.64        10.59         7.69 
TCGA-H4-A2HO 
        1.51 

$subtype4
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V 
       19.00        26.10        12.16        17.85        14.89         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-DK-A1A6 TCGA-DK-A1AC 
        8.25         5.88         2.04         0.43        31.40       118.88 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-E5-A2PC TCGA-G2-A2EO TCGA-G2-A2ES 
        7.17         7.76        36.43        32.78        17.26 

subtype1 subtype2 subtype3 subtype4 
    5.65     1.81     0.46     0.43 
subtype1 subtype2 subtype3 subtype4 
   49.91   100.47    19.46   118.88 
subtype1 subtype2 subtype3 subtype4 
  10.885    5.455    6.640   14.890 
[1] "5.7 - 49.9 (10.9)"  "1.8 - 100.5 (5.5)"  "0.5 - 19.5 (6.6)"  
[4] "0.4 - 118.9 (14.9)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype4"
[25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
[31] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[49] "subtype4" "subtype3" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype4"
[25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
[31] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[49] "subtype4" "subtype3" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype4" "subtype3" "subtype4"
[25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
[31] "subtype3" "subtype4" "subtype2" "subtype4" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype4" "subtype4" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[49] "subtype4" "subtype3" "subtype3" "subtype1"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  6  6
  subtype2  5  5
  subtype3  5  9
  subtype4  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    6
  subtype2    5    5
  subtype3    5    9
  subtype4    5   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        5        5        5
  MALE          6        5        9       12
D3V4, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        1        1        4 
[1] "subtype4" "subtype4" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[8] "subtype4" "subtype4"
D3V5, continuous
D3V6, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        1        1 
character(0)
          vv
clus       MX
  subtype1  2
  subtype2  0
  subtype3  1
  subtype4  1
[1] "NOT AVAILABLE: table dimension [4x1]"
          vv
clus       N0 N1 N2
  subtype1  2  0  0
  subtype2  0  0  0
  subtype3  0  0  1
  subtype4  0  1  0
D3V8, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        1        1 
character(0)
D3V9, continuous
D3V10, continuous
          vv
clus       STAGE III STAGE IV
  subtype1         2        0
  subtype2         0        0
  subtype3         0        0
  subtype4         0        1
D3V11, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype4 
       2        1 
character(0)

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5  9
  subtype2 10  5
  subtype3 17  6
subtype1 subtype2 subtype3 
      14       15       23 
subtype1 subtype2 subtype3 
       9        5        6 
$subtype1
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       19.00        26.10        12.16        14.89         8.61         5.06 
TCGA-BT-A20X TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2I2 
        8.25         2.04         0.43       118.88         7.17         7.76 
TCGA-E5-A2PC TCGA-G2-A2ES 
       36.43        17.26 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20W TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CU-A0YN 
        7.33         6.58         8.35         8.98         1.94        12.92 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-G2-A2EC TCGA-G2-A2EF 
        8.91         5.85         8.81         8.32        13.71        49.91 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-H4-A2HQ 
       26.50         5.65         6.71 

$subtype3
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.79         2.66        11.93        17.85        19.46         5.06 
TCGA-BT-A2LA TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-DK-A1A3 
        5.88         2.89         2.01         0.46         0.69         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2HX 
        2.14        31.40         7.04       100.47         6.64         1.81 
TCGA-DK-A2I1 TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GD-A2C5 TCGA-H4-A2HO 
       10.59        26.93        32.78         7.69         1.51 

subtype1 subtype2 subtype3 
    0.43     1.94     0.46 
subtype1 subtype2 subtype3 
  118.88    49.91   100.47 
subtype1 subtype2 subtype3 
  10.385    8.350    6.640 
[1] "0.4 - 118.9 (10.4)" "1.9 - 49.9 (8.3)"   "0.5 - 100.5 (6.6)" 
 [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype3" "subtype3" "subtype2"
 [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype3" "subtype3" "subtype2"
 [1] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype1" "subtype3" "subtype3" "subtype2"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  5  9
  subtype2  9  6
  subtype3  7 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    9
  subtype2    9    6
  subtype3    7   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        9        7
  MALE          9        6       17
D4V4, continuous
D4V5, continuous
D4V6, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        2        1 
character(0)
          vv
clus       MX
  subtype1  1
  subtype2  2
  subtype3  1
[1] "NOT AVAILABLE: table dimension [3x1]"
          vv
clus       N0 N1 N2
  subtype1  0  1  0
  subtype2  2  0  0
  subtype3  0  0  1
D4V8, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        2        1 
character(0)
D4V9, continuous
D4V10, continuous
          vv
clus       STAGE III STAGE IV
  subtype1         0        1
  subtype2         2        0
  subtype3         0        0
D4V11, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 
       1        2 
character(0)

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 33  7
  subtype2 14  7
  subtype3 28 12
  subtype4 17  6
subtype1 subtype2 subtype3 subtype4 
      40       21       40       23 
subtype1 subtype2 subtype3 subtype4 
       7        7       12        6 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PH TCGA-C4-A0F6 
       12.79        17.85        14.89         8.35         4.64         2.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.46         0.69         4.90         7.20         5.19         8.09 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A3IK 
       31.40         8.98         7.04       100.47         6.64         2.20 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV TCGA-E7-A3Y1 TCGA-FD-A3NA TCGA-FD-A43N 
        3.98        37.84         9.67         0.10        32.02         7.89 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GC-A3BM 
        2.33        13.71         5.65        32.78        20.12         2.86 
TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        1.02         7.69         2.10         3.22         4.37         6.41 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         6.64         5.33         1.51 

$subtype2
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LA TCGA-C4-A0EZ 
        7.33         6.74         6.58        19.00         5.88         8.98 
TCGA-DK-A1AC TCGA-FD-A3SJ TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3VY 
      118.88        24.30        15.16         4.08        26.93         0.82 
TCGA-GC-A3RB TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        4.50         5.82         6.38         6.15         5.69         7.79 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-K4-A3WV 
        4.11         6.71         4.64 

$subtype3
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
        2.66        11.93        26.10         8.61         5.06         8.25 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AE 
        1.94         0.43        12.92         5.46         8.91         7.17 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3WW TCGA-DK-A3WX 
        7.76        75.32         7.82         8.22         8.28        10.55 
TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       36.43         8.81         8.32         8.94         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-G2-A2EF 
        8.94         7.96         6.81         5.49         1.94        49.91 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC 
       26.50        17.26         7.04         2.24         1.38         2.50 
TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GV-A40E 
        1.08         3.12         7.56         6.38 

$subtype4
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LD TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.16        19.46         5.06         3.65         2.53         2.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IT TCGA-DK-A3IU 
        5.85         1.81        10.59       123.85         5.52        11.51 
TCGA-DK-A3WY TCGA-FD-A3B8 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ 
      131.15        11.05        10.98         6.12         4.54        46.78 
TCGA-FD-A3SR TCGA-FD-A43U TCGA-GC-A3OO TCGA-K4-A3WS TCGA-K4-A3WU 
       19.79         6.84         1.32         8.71         3.42 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.82     0.43     1.32 
subtype1 subtype2 subtype3 subtype4 
  100.47   118.88    75.32   131.15 
subtype1 subtype2 subtype3 subtype4 
    6.64     6.58     7.79     6.84 
[1] "0.1 - 100.5 (6.6)" "0.8 - 118.9 (6.6)" "0.4 - 75.3 (7.8)" 
[4] "1.3 - 131.2 (6.8)"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype4" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype1" "subtype3" "subtype3" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype4" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[121] "subtype2" "subtype4" "subtype4" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype4" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype1" "subtype3" "subtype3" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype4" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[121] "subtype2" "subtype4" "subtype4" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype4"
 [13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype4" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
 [37] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype4"
 [43] "subtype1" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype1" "subtype3" "subtype3" "subtype4" "subtype3"
 [61] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype1" "subtype2" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
 [79] "subtype3" "subtype1" "subtype4" "subtype2" "subtype2" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype4" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[109] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[121] "subtype2" "subtype4" "subtype4" "subtype2"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 10 35
  subtype2  5 16
  subtype3 13 28
  subtype4  6 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   35
  subtype2    5   16
  subtype3   13   28
  subtype4    6   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10        5       13        6
  MALE         35       16       28       18
D5V4, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      17        7       12        2 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
D5V5, continuous
D5V6, continuous
          vv
clus       M0 M1 MX
  subtype1 14  0 12
  subtype2  4  0  8
  subtype3  9  0 16
  subtype4  6  2  8
D5V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1 13  2  7  0  3
  subtype2  6  1  2  1  2
  subtype3 16  5  0  1  3
  subtype4  9  1  5  1  0
D5V8, multiclass
D5V9, continuous
D5V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1       12         5        8
  subtype2        4         5        4
  subtype3        7        11        7
  subtype4        3         5        7
D5V11, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 20  9
  subtype2 33  6
  subtype3 39 17
subtype1 subtype2 subtype3 
      29       39       56 
subtype1 subtype2 subtype3 
       9        6       17 
$subtype1
TCGA-BL-A13J TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-CF-A1HR TCGA-CU-A0YO 
        2.66        19.46         5.06        14.89         0.46         4.90 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
        2.53         2.14       100.47         5.85         1.81        10.59 
TCGA-DK-A3IL TCGA-DK-A3IT TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        3.98         5.52        24.30        10.98         6.12        46.78 
TCGA-FD-A3SR TCGA-FD-A43U TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO 
       19.79         6.84        13.71         5.65        32.78         1.32 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WS TCGA-K4-A3WU 
        7.69         2.10         4.37         8.71         3.42 

$subtype2
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A3PH TCGA-C4-A0F6 
       12.79        26.10        17.85         8.35         4.64         2.01 
TCGA-CF-A27C TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 
        0.69         7.20         5.19         8.09        31.40         8.98 
TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-E5-A2PC 
        7.04         6.64         2.20        37.84         9.67        36.43 
TCGA-E7-A3Y1 TCGA-FD-A3NA TCGA-FD-A43N TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A3IE 
        0.10        32.02         7.89         4.08         2.33        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GU-A42P 
        0.82         2.86         4.50         1.02         3.12         6.38 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        3.22         6.41         6.15         7.63         7.79         6.64 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        5.33         1.51         6.71 

$subtype3
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74         6.58        11.93        19.00        12.16 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-C4-A0EZ 
        8.61         5.06         8.25         5.88         3.65         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AC 
        1.94         0.43        12.92         5.46         8.91       118.88 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN 
        7.17         7.76       123.85        75.32         7.82         8.22 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 
       11.51         8.28        10.55       131.15         8.81         8.32 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        11.05         8.94         7.96 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-G2-A2EF 
        6.81         5.49         4.54         1.94        15.16        49.91 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC 
       26.50        26.93        17.26         7.04         2.24         1.38 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A3JZ TCGA-GV-A3QI 
        2.50         1.08         5.82         7.56         5.69         4.11 
TCGA-GV-A40E TCGA-K4-A3WV 
        6.38         4.64 

subtype1 subtype2 subtype3 
    0.46     0.10     0.43 
subtype1 subtype2 subtype3 
  100.47    37.84   131.15 
subtype1 subtype2 subtype3 
    5.85     6.64     7.79 
[1] "0.5 - 100.5 (5.8)" "0.1 - 37.8 (6.6)"  "0.4 - 131.2 (7.8)"
  [1] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [97] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype3"
  [1] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [97] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype3"
  [1] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [97] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[115] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype3"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  8 21
  subtype2  8 37
  subtype3 18 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   21
  subtype2    8   37
  subtype3   18   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        8       18
  MALE         21       37       39
D6V4, continuous
D6V5, continuous
D6V6, continuous
          vv
clus       M0 M1 MX
  subtype1  3  2  8
  subtype2 17  0 14
  subtype3 13  0 22
D6V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1  4  1  8  0  0
  subtype2 16  4  5  0  5
  subtype3 24  4  1  3  3
D6V8, multiclass
D6V9, continuous
D6V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1        1         2        9
  subtype2       15         8        8
  subtype3       10        16        9
D6V11, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 25  3
  subtype2 39 12
  subtype3 30 18
subtype1 subtype2 subtype3 
      28       51       48 
subtype1 subtype2 subtype3 
       3       12       18 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 
       12.79         2.66        11.93         8.35         3.65         2.89 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 
        7.20         5.19         2.14       118.88        10.59        75.32 
TCGA-DK-A3IK TCGA-DK-A3IT TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FJ-A3Z7 
        2.20         5.52         6.81         1.94         7.89        15.16 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF 
        4.08         0.82         1.08         6.38         4.37         7.63 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WU 
        5.33         1.51         6.71         3.42 

$subtype2
TCGA-BL-A13I TCGA-BT-A20N TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 
        7.33        26.10         5.88         4.64         8.98         2.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1A7 
        0.43         0.69        12.92         5.46        31.40         8.98 
TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WW 
        7.04         6.64         7.76         7.82        37.84         8.28 
TCGA-DK-A3WX TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
       10.55        36.43         8.94         6.87         4.01         8.94 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A43U TCGA-FT-A3EE TCGA-G2-A2EF 
        7.96        32.02         5.49         6.84         2.33        49.91 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       26.50        26.93        32.78        17.26         7.04        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OQ 
        2.86         2.24         4.50         1.38         1.02         3.12 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        7.56         3.22         6.41         6.15         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        4.11         6.64         6.38 

$subtype3
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        19.00        12.16        17.85        19.46 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F0 
        5.06        14.89         8.61         5.06         8.25         1.94 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AB 
        2.04         0.46         4.90         8.09         2.53         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL 
      100.47         7.17         5.85         1.81       123.85         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WY TCGA-E7-A3Y1 
        8.22        10.49        11.51         9.67       131.15         0.10 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        8.81         8.32        11.05        24.30        10.98         6.12 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO 
        4.54        46.78        19.79        13.71         5.65         1.32 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-K4-A3WS TCGA-K4-A3WV 
        2.50         7.69         2.10         5.82         8.71         4.64 

subtype1 subtype2 subtype3 
    0.82     0.43     0.10 
subtype1 subtype2 subtype3 
  118.88    49.91   131.15 
subtype1 subtype2 subtype3 
   5.425    7.040    8.155 
[1] "0.8 - 118.9 (5.4)" "0.4 - 49.9 (7.0)"  "0.1 - 131.2 (8.2)"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [31] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[127] "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [31] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[127] "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
  [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [25] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [31] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [55] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[103] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[127] "subtype3"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  4 28
  subtype2 13 41
  subtype3 17 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   28
  subtype2   13   41
  subtype3   17   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       13       17
  MALE         28       41       31
D7V4, continuous
D7V5, continuous
D7V6, continuous
          vv
clus       M0 M1 MX
  subtype1  8  0 11
  subtype2 15  0 21
  subtype3 11  2 12
D7V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1  8  5  4  2  0
  subtype2 21  4  3  1  6
  subtype3 16  0  7  0  2
D7V8, multiclass
D7V9, continuous
D7V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1        3         4       11
  subtype2       16        12        8
  subtype3        7        11        7
D7V11, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 13  3
  subtype2 41 19
  subtype3  6  1
  subtype4 28  8
  subtype5  6  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       60        7       36        8 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3       19        1        8        2 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 
       12.79         2.66        11.93         8.35         3.65         2.89 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF 
        2.14       118.88        15.16         6.38         4.37         7.63 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WU 
        5.33         1.51         6.71         3.42 

$subtype2
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        26.10        12.16 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-C4-A0F6 
        8.61         5.06         8.25         5.88         8.98         2.01 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 
        2.04         0.43         0.69        12.92         8.09        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A3IS 
        8.98         7.04         6.64         7.76         8.22        37.84 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-FD-A3B5 
        9.67         8.28        10.55        36.43         0.10         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43U 
        6.87         8.94         7.96        32.02         6.12         6.84 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        2.33        49.91        26.50        26.93        32.78        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD 
        7.04        20.12         2.86         2.24         4.50         1.02 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12         5.82         7.56         3.22         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WV 
        5.69         7.79         4.11         6.64         6.38         4.64 

$subtype3
TCGA-BT-A3PH TCGA-CU-A3QU TCGA-FD-A3SS TCGA-FD-A43N TCGA-FJ-A3ZF TCGA-G2-A3VY 
        4.64         5.19         1.94         7.89         4.08         0.82 
TCGA-GC-A3YS 
        1.08 

$subtype4
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.85        19.46         5.06        14.89         1.94         0.46 
TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        4.90         2.53         8.91       100.47         7.17         5.85 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ 
        1.81        10.59       123.85         2.20         3.98        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
        5.52        11.51       131.15         8.81         8.32        11.05 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-G2-A2EC 
       24.30        10.98         4.54        46.78        19.79        13.71 
TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-K4-A3WS 
        5.65         1.32         2.50         7.69         2.10         8.71 

$subtype5
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-FD-A3B7 TCGA-FD-A3SN 
        7.20         5.46        75.32         7.82         4.01         6.81 
TCGA-FD-A3SO TCGA-GC-A3RC 
        5.49         1.38 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.51     0.10     0.82     0.46     1.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  118.88    49.91     7.89   131.15    75.32 
subtype1 subtype2 subtype3 subtype4 subtype5 
   5.855    7.185    4.080    8.515    6.150 
[1] "1.5 - 118.9 (5.9)" "0.1 - 49.9 (7.2)"  "0.8 - 7.9 (4.1)"  
[4] "0.5 - 131.2 (8.5)" "1.4 - 75.3 (6.2)" 
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype1" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [31] "subtype5" "subtype5" "subtype3" "subtype2" "subtype4" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [49] "subtype4" "subtype5" "subtype4" "subtype4" "subtype5" "subtype2"
 [55] "subtype4" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [67] "subtype2" "subtype2" "subtype5" "subtype4" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype4" "subtype2" "subtype5" "subtype5"
 [79] "subtype4" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype2"
 [91] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
[103] "subtype2" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[127] "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype1" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [31] "subtype5" "subtype5" "subtype3" "subtype2" "subtype4" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [49] "subtype4" "subtype5" "subtype4" "subtype4" "subtype5" "subtype2"
 [55] "subtype4" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [67] "subtype2" "subtype2" "subtype5" "subtype4" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype4" "subtype2" "subtype5" "subtype5"
 [79] "subtype4" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype2"
 [91] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
[103] "subtype2" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[127] "subtype2"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [19] "subtype1" "subtype3" "subtype2" "subtype4" "subtype1" "subtype2"
 [25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [31] "subtype5" "subtype5" "subtype3" "subtype2" "subtype4" "subtype1"
 [37] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
 [49] "subtype4" "subtype5" "subtype4" "subtype4" "subtype5" "subtype2"
 [55] "subtype4" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
 [61] "subtype2" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
 [67] "subtype2" "subtype2" "subtype5" "subtype4" "subtype2" "subtype2"
 [73] "subtype2" "subtype4" "subtype4" "subtype2" "subtype5" "subtype5"
 [79] "subtype4" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype4" "subtype2" "subtype2"
 [91] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
[103] "subtype2" "subtype4" "subtype3" "subtype4" "subtype4" "subtype2"
[109] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[121] "subtype2" "subtype1" "subtype1" "subtype1" "subtype4" "subtype1"
[127] "subtype2"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  3 17
  subtype2 17 46
  subtype3  0  7
  subtype4 14 22
  subtype5  0  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   17
  subtype2   17   46
  subtype3    0    7
  subtype4   14   22
  subtype5    0    8
D8V4, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       26        2        4        1 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [7] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype4"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
D8V5, continuous
D8V6, continuous
          vv
clus       M0 M1 MX
  subtype1  4  0  7
  subtype2 17  1 20
  subtype3  2  0  4
  subtype4  8  1 10
  subtype5  3  0  3
D8V7, multiclass
          vv
clus       N0 N1 N2 N3 NX
  subtype1  4  3  3  1  0
  subtype2 22  3  3  1  8
  subtype3  2  2  1  1  0
  subtype4 12  0  7  0  0
  subtype5  5  1  0  0  0
D8V8, multiclass
D8V9, continuous
D8V10, continuous
          vv
clus       STAGE II STAGE III STAGE IV
  subtype1        2         1        6
  subtype2       19        12        7
  subtype3        1         2        4
  subtype4        3         9        7
  subtype5        1         3        2
D8V11, multiclass
                            V1.D                               V2 
                 "Time to Death"                            "AGE" 
                              V3                               V4 
                        "GENDER"    "KARNOFSKY.PERFORMANCE.SCORE" 
                              V5                               V6 
         "NUMBERPACKYEARSSMOKED" "TOBACCOSMOKINGHISTORYINDICATOR" 
                              V7                               V8 
            "DISTANT.METASTASIS"          "LYMPH.NODE.METASTASIS" 
                              V9                              V10 
         "NUMBER.OF.LYMPH.NODES"                "TUMOR.STAGECODE" 
                             V11 
         "NEOPLASM.DISEASESTAGE" 
> q(save="no")
