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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.73.3976/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.73.3976/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/BLCA/1929617/1.GDAC_mergedClustering.Finished/BLCA.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA/1708518/1.GDAC_clinicalDataPicker.Finished/BLCA.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=69, in cluster file=92, common to both=68
[1]  8 68
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
 7 18  9 16 15 
 1  2  3  4  5 
 7 18  9 16 15 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
17 27 21 
 1  2  3 
17 27 21 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
12 10 13 16 
 1  2  3  4 
12 10 13 16 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
14 17 20 
 1  2  3 
14 17 20 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
27 16 22 
 1  2  3 
27 16 22 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
23  7 35 
 1  2  3 
23  7 35 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
12 29 11  3 12 
 1  2  3  4  5 
12 29 11  3 12 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 2 12 53 
 2  3 
12 53 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NEOADJUVANTTHERAPY"                    
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 68 columns.

[1] "Batch" "13"   
[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-C4-A0EZ 
          NA           NA           NA           NA           NA           NA 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
          59           88           61           NA           14           13 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 
          21           NA           NA          219           77           NA 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
         955          273          214          271         3616         3056 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
         218          178          202           55          322           NA 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        2291         1151         1108          268          253           NA 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
         209           NA          336           71          417         1497 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
         806          172           NA          684          525          214 
TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
          NA           68          234          160          187          160 
TCGA-H4-A2HO TCGA-H4-A2HQ 
          46          204 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 68 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  4  3
  subtype2 10  8
  subtype3  6  3
  subtype4 12  4
  subtype5  9  6
subtype1 subtype2 subtype3 subtype4 subtype5 
       7       18        9       16       15 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        8        3        4        6 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20W TCGA-CU-A0YR TCGA-DK-A2I1 TCGA-G2-A3IE 
       12.79        26.10         8.35         7.20        10.59        20.12 
TCGA-H4-A2HQ 
        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-A20X TCGA-C4-A0F0 TCGA-CU-A0YO TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF 
        8.25         1.94         4.90         7.04         7.17         5.85 
TCGA-DK-A1AG TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-G2-A2EK TCGA-H4-A2HO 
        6.64         8.32         4.01        11.05         5.65         1.51 

$subtype3
TCGA-BL-A13J TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I6 
        2.66         0.46         2.53         2.14         1.81        75.32 
TCGA-FD-A3B5 TCGA-FT-A3EE TCGA-GD-A2C5 
        8.94         2.33         7.69 

$subtype4
TCGA-BL-A3JM TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F6 TCGA-CF-A27C 
        6.74        17.85        19.46        14.89         2.01         0.69 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A3IS TCGA-E5-A2PC TCGA-G2-A2EJ TCGA-G2-A2EO 
       31.40         8.91        37.84        36.43        26.50        22.49 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GV-A3JW 
       17.26         7.04         2.24         5.26 

$subtype5
TCGA-BT-A20R TCGA-BT-A20V TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A1A7 
        5.06         5.06         8.98         0.43        12.30         8.98 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-G2-A2EF 
      118.88       100.47         7.76         8.81         6.87        49.22 
TCGA-G2-A2EL TCGA-GV-A3JX TCGA-GV-A3JZ 
       26.93         6.15         5.26 

subtype1 subtype2 subtype3 subtype4 subtype5 
    6.71     1.51     0.46     0.69     0.43 
subtype1 subtype2 subtype3 subtype4 subtype5 
   26.10    19.00    75.32    37.84   118.88 
subtype1 subtype2 subtype3 subtype4 subtype5 
  10.590    7.105    2.530   16.075    8.810 
[1] "6.7 - 26.1 (10.6)" "1.5 - 19.0 (7.1)"  "0.5 - 75.3 (2.5)" 
[4] "0.7 - 37.8 (16.1)" "0.4 - 118.9 (8.8)"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype5"
[13] "subtype4" "subtype2" "subtype5" "subtype1" "subtype2" "subtype5"
[19] "subtype2" "subtype4" "subtype3" "subtype5" "subtype4" "subtype5"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype5"
[31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype5" "subtype3" "subtype4"
[43] "subtype4" "subtype5" "subtype2" "subtype3" "subtype5" "subtype2"
[49] "subtype2" "subtype3" "subtype5" "subtype4" "subtype2" "subtype5"
[55] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[61] "subtype4" "subtype5" "subtype5" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype5"
[13] "subtype4" "subtype2" "subtype5" "subtype1" "subtype2" "subtype5"
[19] "subtype2" "subtype4" "subtype3" "subtype5" "subtype4" "subtype5"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype5"
[31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype5" "subtype3" "subtype4"
[43] "subtype4" "subtype5" "subtype2" "subtype3" "subtype5" "subtype2"
[49] "subtype2" "subtype3" "subtype5" "subtype4" "subtype2" "subtype5"
[55] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[61] "subtype4" "subtype5" "subtype5" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype2" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype4" "subtype4" "subtype5"
[13] "subtype4" "subtype2" "subtype5" "subtype1" "subtype2" "subtype5"
[19] "subtype2" "subtype4" "subtype3" "subtype5" "subtype4" "subtype5"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype4" "subtype5"
[31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype5" "subtype3" "subtype4"
[43] "subtype4" "subtype5" "subtype2" "subtype3" "subtype5" "subtype2"
[49] "subtype2" "subtype3" "subtype5" "subtype4" "subtype2" "subtype5"
[55] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[61] "subtype4" "subtype5" "subtype5" "subtype2" "subtype1"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  2  5
  subtype2  5 13
  subtype3  3  6
  subtype4  5 11
  subtype5  7  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    5
  subtype2    5   13
  subtype3    3    6
  subtype4    5   11
  subtype5    7    8
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        1        1        8        5 
 [1] "subtype5" "subtype4" "subtype4" "subtype5" "subtype4" "subtype5"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype5"
[13] "subtype5"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 13  4
  subtype2 14 13
  subtype3 14  7
subtype1 subtype2 subtype3 
      17       27       21 
subtype1 subtype2 subtype3 
       4       13        7 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A20W TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-DK-A1A3 
       12.79         5.06         8.35         8.98         2.01         2.53 
TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-E5-A2PC TCGA-FT-A3EE 
       31.40       118.88       100.47        10.59        36.43         2.33 
TCGA-G2-A2EK TCGA-G2-A3IE TCGA-GD-A2C5 TCGA-H4-A2HO TCGA-H4-A2HQ 
        5.65        20.12         7.69         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        12.30 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I6 
        4.90         7.20         8.91         5.85         7.76        75.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.81         8.32         8.94         6.87         4.01        11.05 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
       49.22        26.50        26.93 

$subtype3
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-C4-A0F7 
        2.66        26.10        17.85        19.46        14.89         2.04 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE 
        0.46         0.69         2.14         8.98         7.04         7.17 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-G2-A2EC TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        6.64         1.81        13.71        22.49        17.26         7.04 
TCGA-GC-A3I6 TCGA-GV-A3JW TCGA-GV-A3JX 
        2.24         5.26         6.15 

subtype1 subtype2 subtype3 
    1.51     0.43     0.46 
subtype1 subtype2 subtype3 
  118.88    75.32    26.10 
subtype1 subtype2 subtype3 
    8.35     8.32     7.04 
[1] "1.5 - 118.9 (8.3)" "0.4 - 75.3 (8.3)"  "0.5 - 26.1 (7.0)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  8  9
  subtype2 11 16
  subtype3  4 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    9
  subtype2   11   16
  subtype3    4   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       11        4
  MALE          9       16       17
D2V4, continuous

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  8  4
  subtype2  5  5
  subtype3 11  2
  subtype4  7  9
subtype1 subtype2 subtype3 subtype4 
      12       10       13       16 
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        12.30         8.81         8.32 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-H4-A2HQ 
       13.71        49.22        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-C4-A0F7 TCGA-CF-A1HS TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AE 
        8.25         2.04         0.43        31.40       118.88         7.17 
TCGA-DK-A2I2 TCGA-E5-A2PC TCGA-G2-A2EO TCGA-G2-A2ES 
        7.76        36.43        22.49        17.26 

subtype1 subtype2 subtype3 subtype4 
    5.65     1.81     0.46     0.43 
subtype1 subtype2 subtype3 subtype4 
   49.22   100.47    19.46   118.88 
subtype1 subtype2 subtype3 subtype4 
  10.640    5.455    6.640   16.075 
[1] "5.7 - 49.2 (10.6)"  "1.8 - 100.5 (5.5)"  "0.5 - 19.5 (6.6)"  
[4] "0.4 - 118.9 (16.1)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype4" "subtype2" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype4" "subtype2" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[13] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype4" "subtype2" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype4" "subtype4" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype3" "subtype1"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  6  6
  subtype2  5  5
  subtype3  5  8
  subtype4  5 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    6
  subtype2    5    5
  subtype3    5    8
  subtype4    5   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        5        5        5
  MALE          6        5        8       11
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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  9  5
  subtype2  7 10
  subtype3 15  5
subtype1 subtype2 subtype3 
      14       17       20 
subtype1 subtype2 subtype3 
       5       10        5 
$subtype1
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        12.30 
TCGA-DK-A1AF TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        5.85         8.81         8.32        13.71        49.22        26.50 
TCGA-G2-A2EK TCGA-H4-A2HQ 
        5.65         6.71 

$subtype2
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20T 
        2.66        19.00        26.10        12.16         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-CF-A1HS TCGA-DK-A1A3 TCGA-DK-A1AC 
        8.61         5.06         8.25         0.43         2.53       118.88 
TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-E5-A2PC TCGA-G2-A2ES 
        7.17         1.81         7.76        36.43        17.26 

$subtype3
TCGA-BL-A0C8 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-C4-A0F1 TCGA-C4-A0F6 
       12.79        11.93        17.85        19.46         2.89         2.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A27C TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        2.04         0.46         0.69         2.14        31.40         7.04 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-G2-A2EL TCGA-G2-A2EO 
        8.91       100.47         6.64        10.59        26.93        22.49 
TCGA-GD-A2C5 TCGA-H4-A2HO 
        7.69         1.51 

subtype1 subtype2 subtype3 
    1.94     0.43     0.46 
subtype1 subtype2 subtype3 
   49.22   118.88   100.47 
subtype1 subtype2 subtype3 
   8.335    8.250    8.300 
[1] "1.9 - 49.2 (8.3)"  "0.4 - 118.9 (8.2)" "0.5 - 100.5 (8.3)"
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype1"
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype1"
 [1] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[49] "subtype3" "subtype3" "subtype1"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  8  6
  subtype2  7 10
  subtype3  6 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2    7   10
  subtype3    6   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        7        6
  MALE          6       10       14
D4V4, continuous

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 20  7
  subtype2  7  9
  subtype3 15  7
subtype1 subtype2 subtype3 
      27       16       22 
subtype1 subtype2 subtype3 
       7        9        7 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
       12.79         2.66        17.85        19.46        14.89         8.35 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A6 
        2.01         0.46         0.69         4.90         7.20        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A3IS TCGA-FT-A3EE 
        8.98         7.04       100.47         6.64        37.84         2.33 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GD-A2C5 TCGA-GV-A3JW 
       13.71         5.65        22.49        20.12         7.69         5.26 
TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.15         1.51         6.71 

$subtype2
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R 
        7.33         6.74         6.58        19.00        12.16         5.06 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
        2.53         2.14       118.88         5.85         1.81        10.59 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-G2-A2EL TCGA-GV-A3JZ 
        4.01        11.05        26.93         5.26 

$subtype3
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F0 
       11.93        26.10         8.61         5.06         8.25         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I6 
        0.43        12.30         8.91         7.17         7.76        75.32 
TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-G2-A2EF 
       36.43         8.81         8.32         8.94         6.87        49.22 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 
       26.50        17.26         7.04         2.24 

subtype1 subtype2 subtype3 
    0.46     1.81     0.43 
subtype1 subtype2 subtype3 
  100.47   118.88    75.32 
subtype1 subtype2 subtype3 
    7.20     6.66     8.71 
[1] "0.5 - 100.5 (7.2)" "1.8 - 118.9 (6.7)" "0.4 - 75.3 (8.7)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[55] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  7 20
  subtype2  5 11
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   20
  subtype2    5   11
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7        5       10
  MALE         20       11       12
D5V4, continuous

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 15  8
  subtype2  2  5
  subtype3 25 10
subtype1 subtype2 subtype3 
      23        7       35 
subtype1 subtype2 subtype3 
       8        5       10 
$subtype1
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20X TCGA-C4-A0F0 
        7.33        11.93        12.16         8.61         8.25         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I6 
        0.43        12.30         8.91         7.17         7.76        75.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.81         8.32         8.94         6.87         4.01        11.05 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 
       49.22        26.50        17.26         7.04         2.24 

$subtype2
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20V TCGA-DK-A1AC TCGA-G2-A2EL 
        6.74         6.58        19.00         5.06       118.88        26.93 
TCGA-GV-A3JZ 
        5.26 

$subtype3
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.79         2.66        26.10        17.85        19.46         5.06 
TCGA-BT-A20T TCGA-BT-A20W TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YO 
       14.89         8.35         2.01         0.46         0.69         4.90 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        7.20         2.53         2.14        31.40         8.98         7.04 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IS 
      100.47         5.85         6.64         1.81        10.59        37.84 
TCGA-E5-A2PC TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE 
       36.43         2.33        13.71         5.65        22.49        20.12 
TCGA-GD-A2C5 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.69         5.26         6.15         1.51         6.71 

subtype1 subtype2 subtype3 
    0.43     5.06     0.46 
subtype1 subtype2 subtype3 
   75.32   118.88   100.47 
subtype1 subtype2 subtype3 
    8.61     6.74     7.04 
[1] "0.4 - 75.3 (8.6)"  "5.1 - 118.9 (6.7)" "0.5 - 100.5 (7.0)"
 [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  9 14
  subtype2  1  6
  subtype3 12 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   14
  subtype2    1    6
  subtype3   12   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        1       12
  MALE         14        6       23
D6V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       6        2        9 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype3"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  8  4
  subtype2 15 14
  subtype3  8  3
  subtype4  1  2
  subtype5 10  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      12       29       11        3       12 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4       14        3        2        2 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20T TCGA-BT-A20W TCGA-CU-A0YR 
       12.79         2.66        11.93        14.89         8.35         7.20 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-H4-A2HO TCGA-H4-A2HQ 
        2.14       118.88        10.59        75.32         1.51         6.71 

$subtype2
TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V 
        7.33        19.00        26.10        12.16         8.61         5.06 
TCGA-BT-A20X TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS 
        8.25         8.98         1.94         2.89         2.04         0.43 
TCGA-CU-A0YN TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-FD-A3B4 
       12.30         8.98         7.17         6.64         7.76         8.32 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         6.87         4.01         2.33        49.22        26.50 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 
       26.93        22.49        17.26         7.04         2.24 

$subtype3
TCGA-BL-A3JM TCGA-BT-A20P TCGA-C4-A0F6 TCGA-CF-A27C TCGA-DK-A1A6 TCGA-DK-A1AA 
        6.74        17.85         2.01         0.69        31.40         7.04 
TCGA-DK-A3IS TCGA-E5-A2PC TCGA-G2-A2EC TCGA-G2-A3IE TCGA-GV-A3JW 
       37.84        36.43        13.71        20.12         5.26 

$subtype4
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-GV-A3JX 
        6.58         5.06         6.15 

$subtype5
TCGA-BT-A20Q TCGA-CF-A1HR TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AD 
       19.46         0.46         4.90         2.53         8.91       100.47 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-G2-A2EK TCGA-GD-A2C5 
        5.85         1.81         8.81        11.05         5.65         7.69 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.51     0.43     0.69     5.06     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
  118.88    49.22    37.84     6.58   100.47 
subtype1 subtype2 subtype3 subtype4 subtype5 
    9.47     8.25    13.71     6.15     6.77 
[1] "1.5 - 118.9 (9.5)" "0.4 - 49.2 (8.2)"  "0.7 - 37.8 (13.7)"
[4] "5.1 - 6.6 (6.2)"   "0.5 - 100.5 (6.8)"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype3" "subtype5" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype5" "subtype2" "subtype3" "subtype2"
[55] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype3" "subtype2" "subtype5" "subtype3" "subtype4" "subtype1"
[67] "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype3" "subtype5" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype5" "subtype2" "subtype3" "subtype2"
[55] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype3" "subtype2" "subtype5" "subtype3" "subtype4" "subtype1"
[67] "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype5" "subtype4"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype2"
[25] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype1"
[31] "subtype3" "subtype2" "subtype3" "subtype5" "subtype1" "subtype5"
[37] "subtype2" "subtype5" "subtype2" "subtype5" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype3" "subtype5" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype5" "subtype2" "subtype3" "subtype2"
[55] "subtype2" "subtype5" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype3" "subtype2" "subtype5" "subtype3" "subtype4" "subtype1"
[67] "subtype1"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  3  9
  subtype2 10 19
  subtype3  4  7
  subtype4  1  2
  subtype5  5  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    9
  subtype2   10   19
  subtype3    4    7
  subtype4    1    2
  subtype5    5    7
D7V4, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       8        5        1        2 
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype3"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype2  9  3
  subtype3 32 21
subtype2 subtype3 
      12       53 
subtype2 subtype3 
       3       21 
$subtype2
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-CU-A0YR TCGA-DK-A1A5 
       12.79         2.66        11.93         8.35         7.20         2.14 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-H4-A2HO TCGA-H4-A2HQ 
      118.88         1.81        10.59        75.32         1.51         6.71 

$subtype3
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-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.85        19.46         5.06        14.89         8.61         5.06 
TCGA-BT-A20X TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
        8.25         8.98         1.94         2.89         2.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A1A3 
        0.46         0.43         0.69        12.30         4.90         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       31.40         8.98         7.04         8.91       100.47         7.17 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-E5-A2PC TCGA-FD-A3B3 
        5.85         6.64         7.76        37.84        36.43         8.81 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FT-A3EE TCGA-G2-A2EC 
        8.32         8.94         6.87        11.05         2.33        13.71 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       49.22        26.50         5.65        26.93        22.49        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GV-A3JW 
        7.04        20.12         2.24         7.69         5.26 

subtype2 subtype3 
    1.51     0.43 
subtype2 subtype3 
  118.88   100.47 
subtype2 subtype3 
   7.775    8.250 
[1] "1.5 - 118.9 (7.8)" "0.4 - 100.5 (8.2)"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[1] "hr=" "1.4"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype2  4  8
  subtype3 19 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    4    8
  subtype3   19   34
        clus
vv       subtype2 subtype3
  FEMALE        4       19
  MALE          8       34
D8V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       1       14 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3"
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
> q(save="no")
