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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/SARC-TP/4431599/SARC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SARC-TP/4401947/SARC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=SARC-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=SARC-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SARC-TP/4401947/SARC-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/SARC-TP/4431599/SARC-TP.mergedcluster.txt"

nPatients in clinical file=74, in cluster file=98, common to both=66
[1]  8 66
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
18 19  8 12 
 1  2  3  4 
18 19  8 12 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
22 19 16 
 1  2  3 
22 19 16 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
11  9 13  1  8  8 
 1  2  3  5  6 
11  9 13  8  8 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 2  3 
16 34 
 2  3 
16 34 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
 6 30 12 18 
 1  2  3  4 
 6 30 12 18 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 2 27 37 
 2  3 
27 37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
13 30 23 
 1  2  3 
13 30 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 2  3 
36 30 
 2  3 
36 30 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "YEARSTOBIRTH"                          
[2] "VITALSTATUS"                           
[3] "DAYSTODEATH"                           
[4] "DAYSTOLASTFOLLOWUP"                    
[5] "DCCUPLOADDATE"                         
[6] "GENDER"                                
[7] "RADIATIONTHERAPY"                      
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "BATCHNUMBER"                           

Input Data has 9 rows and 66 columns.

[1] "Batch" "9"    
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62          827           NA          745           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1291          960          908         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          260 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1620         1309           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3288          520          609          457          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48K 
          NA           NA           NA         1352         1197          587 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
          NA          373          828           14            3            2 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
           2          818           NA          126           NA          650 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
         272           98           42           NA          966           NA 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
        4362         3555           NA         2229           NA          688 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MO-A47R TCGA-PC-A5DK 
         190           NA          356          159            3         2296 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=37, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 14  4
  subtype2 13  6
  subtype3  4  4
  subtype4  8  4
subtype1 subtype2 subtype3 subtype4 
      18       19        8       12 
subtype1 subtype2 subtype3 subtype4 
       4        6        4        4 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        27.19        12.85        46.68        42.44        31.56 
TCGA-DX-A3LS TCGA-DX-A3LY TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        9.01        17.10         0.46         0.07         0.07        26.89 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-MO-A47R 
        8.94         3.22       143.41         5.88        22.62         0.10 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V 
        2.04        24.49        29.85        74.66         5.23        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.78        60.30         8.55         9.70        53.26 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49       108.10        20.02        15.02        17.75 
TCGA-HB-A3YV 
        4.54 

$subtype3
TCGA-DX-A1L0 TCGA-DX-A3U7 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IS-A3KA TCGA-JV-A5VE 
       18.51        42.77         4.14        12.62        13.58         6.25 
TCGA-JV-A5VF TCGA-KF-A41W 
        1.05        11.70 

$subtype4
TCGA-DX-A23U TCGA-DX-A2J4 TCGA-DX-A3U8 TCGA-FX-A3NJ TCGA-IE-A4EH TCGA-IE-A4EK 
       76.37        43.04         4.50         0.10        21.37         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-PC-A5DK 
       25.22        31.76        28.21       116.88        73.28        75.48 

subtype1 subtype2 subtype3 subtype4 
    0.07     2.04     1.05     0.10 
subtype1 subtype2 subtype3 subtype4 
  143.41   108.10    42.77   116.88 
subtype1 subtype2 subtype3 subtype4 
  13.445   23.080   12.160   29.985 
[1] "0.1 - 143.4 (13.4)" "2.0 - 108.1 (23.1)" "1.1 - 42.8 (12.2)" 
[4] "0.1 - 116.9 (30.0)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[43] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
[49] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[43] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
[49] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype4" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[43] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
[49] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype4"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 13  5
  subtype2  4 15
  subtype3  6  2
  subtype4  5  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    5
  subtype2    4   15
  subtype3    6    2
  subtype4    5    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       13        4        6        5
  MALE          5       15        2        7

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 15  7
  subtype2 11  8
  subtype3 13  3
subtype1 subtype2 subtype3 
      22       19       16 
subtype1 subtype2 subtype3 
       7        8        3 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        27.19        24.49        42.44        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 
        5.23        76.37        66.87        27.78        60.30        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
       43.04         9.01        70.49        17.10        15.02        17.75 
TCGA-DX-A3U8 TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IS-A3K7 
        4.50        26.89         3.22       143.41 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
        2.04        12.85        18.51        46.68        74.66         6.28 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-FX-A2QS 
        8.55         9.70        23.08       108.10        20.02         0.46 
TCGA-FX-A3RE TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W 
        0.07         4.54        13.58         5.88         1.05        11.70 
TCGA-MO-A47R 
        0.10 

$subtype3
TCGA-DX-A3U7 TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       42.77         0.10         0.07         4.14        12.62        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        25.22        31.76        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
       73.28        22.62         6.25        75.48 

subtype1 subtype2 subtype3 
    3.22     0.07     0.07 
subtype1 subtype2 subtype3 
  143.41   108.10   116.88 
subtype1 subtype2 subtype3 
  27.485    9.700   21.995 
[1] "3.2 - 143.4 (27.5)" "0.1 - 108.1 (9.7)"  "0.1 - 116.9 (22.0)"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[49] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype2" "subtype2" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  9 13
  subtype2  8 11
  subtype3 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   13
  subtype2    8   11
  subtype3   11    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        8       11
  MALE         13       11        5

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 6 5
  subtype2 7 2
  subtype3 8 5
  subtype5 6 2
  subtype6 6 2
subtype1 subtype2 subtype3 subtype5 subtype6 
      11        9       13        8        8 
subtype1 subtype2 subtype3 subtype5 subtype6 
       5        2        5        2        2 
$subtype1
TCGA-DX-A1KU TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U6 
       14.04         5.23        53.26         9.01        23.08        17.75 
TCGA-DX-A3U8 TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-KF-A41W 
        4.50        26.89       143.41         1.05        11.70 

$subtype2
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-FX-A2QS 
       12.85        74.66         8.55       108.10        20.02         0.46 
TCGA-FX-A3RE TCGA-IW-A3M5 TCGA-MO-A47R 
        0.07         5.88         0.10 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23V 
       24.49        18.51        46.68        42.44        31.56        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        6.28        27.78         9.70        70.49        17.10        15.02 
TCGA-IE-A4EJ 
        3.22 

$subtype5
TCGA-DX-A3U7 TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       42.77         0.10        12.62         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-PC-A5DK 
       31.76        75.48 

$subtype6
TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        4.14        21.37        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE 
       22.62         6.25 

subtype1 subtype2 subtype3 subtype5 subtype6 
    1.05     0.07     3.22     0.10     4.14 
subtype1 subtype2 subtype3 subtype5 subtype6 
  143.41   108.10    70.49    75.48   116.88 
subtype1 subtype2 subtype3 subtype5 subtype6 
  14.040    8.550   24.490   18.920   21.995 
[1] "1.1 - 143.4 (14.0)" "0.1 - 108.1 (8.6)"  "3.2 - 70.5 (24.5)" 
[4] "0.1 - 75.5 (18.9)"  "4.1 - 116.9 (22.0)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype5"
[25] "subtype1" "subtype2" "subtype5" "subtype2" "subtype1" "subtype6"
[31] "subtype5" "subtype6" "subtype5" "subtype3" "subtype5" "subtype5"
[37] "subtype5" "subtype6" "subtype1" "subtype6" "subtype6" "subtype6"
[43] "subtype2" "subtype6" "subtype6" "subtype1" "subtype1" "subtype2"
[49] "subtype5"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype5"
[25] "subtype1" "subtype2" "subtype5" "subtype2" "subtype1" "subtype6"
[31] "subtype5" "subtype6" "subtype5" "subtype3" "subtype5" "subtype5"
[37] "subtype5" "subtype6" "subtype1" "subtype6" "subtype6" "subtype6"
[43] "subtype2" "subtype6" "subtype6" "subtype1" "subtype1" "subtype2"
[49] "subtype5"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype5"
[25] "subtype1" "subtype2" "subtype5" "subtype2" "subtype1" "subtype6"
[31] "subtype5" "subtype6" "subtype5" "subtype3" "subtype5" "subtype5"
[37] "subtype5" "subtype6" "subtype1" "subtype6" "subtype6" "subtype6"
[43] "subtype2" "subtype6" "subtype6" "subtype1" "subtype1" "subtype2"
[49] "subtype5"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  7  4
  subtype2  5  4
  subtype3  3 10
  subtype5  3  5
  subtype6  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    4
  subtype2    5    4
  subtype3    3   10
  subtype5    3    5
  subtype6    8    0

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype2 12  4
  subtype3 22 12
subtype2 subtype3 
      16       34 
subtype2 subtype3 
       4       12 
$subtype2
TCGA-DX-A3U7 TCGA-FX-A3NJ TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI 
       42.77         0.10         4.14        12.62        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
       73.28        22.62         6.25        75.48 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        12.85        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       31.56        74.66         5.23        66.87         6.28        27.78 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.55         9.70        53.26        43.04         9.01        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.10        17.10        20.02        15.02        17.75 
TCGA-DX-A3U8 TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IS-A3K7 
        4.50         0.46         0.07        26.89         3.22       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W TCGA-MO-A47R 
        5.88         1.05        11.70         0.10 

subtype2 subtype3 
    0.10     0.07 
subtype2 subtype3 
  116.88   143.41 
subtype2 subtype3 
  21.995   17.425 
[1] "0.1 - 116.9 (22.0)" "0.1 - 143.4 (17.4)"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2"
[1] "hr=" "1.5"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype2 11  5
  subtype3 15 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2   11    5
  subtype3   15   19
        clus
vv       subtype2 subtype3
  FEMALE       11       15
  MALE          5       19

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  3  3
  subtype2 20 10
  subtype3  8  4
  subtype4 14  4
subtype1 subtype2 subtype3 subtype4 
       6       30       12       18 
subtype1 subtype2 subtype3 subtype4 
       3       10        4        4 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3UA TCGA-IE-A4EJ TCGA-LI-A67I TCGA-MO-A47R 
       14.04        12.85        10.68         3.22         5.23         0.10 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.51        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.23        76.37        66.87        27.78        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.55         9.70        53.26        43.04         9.01        23.08 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-FX-A2QS 
      108.10        20.02        17.75        19.30        12.26         0.46 
TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W 
        4.54       143.41         5.88         6.25         1.05        11.70 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       24.49        46.68         6.28        70.49        17.10        15.02 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-HB-A2OT TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M6 
        4.50        44.45        26.89        28.21        13.58        22.62 

$subtype4
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A48L TCGA-DX-A48O TCGA-FX-A3NJ 
       42.77        14.99        39.35        24.26        27.22         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI 
        0.07         0.07         4.14        12.62        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-PC-A5DK 
        1.38        25.22        31.76       116.88        73.28        75.48 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.46     4.50     0.07 
subtype1 subtype2 subtype3 subtype4 
   14.04   143.41    70.49   116.88 
subtype1 subtype2 subtype3 subtype4 
   7.955   19.660   23.555   22.815 
[1] "0.1 - 14.0 (8.0)"   "0.5 - 143.4 (19.7)" "4.5 - 70.5 (23.6)" 
[4] "0.1 - 116.9 (22.8)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype4"
[31] "subtype3" "subtype4" "subtype1" "subtype3" "subtype4" "subtype2"
[37] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[49] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype3"
[55] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype4"
[31] "subtype3" "subtype4" "subtype1" "subtype3" "subtype4" "subtype2"
[37] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[49] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype3"
[55] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype4"
[31] "subtype3" "subtype4" "subtype1" "subtype3" "subtype4" "subtype2"
[37] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[43] "subtype4" "subtype3" "subtype2" "subtype4" "subtype4" "subtype4"
[49] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype3"
[55] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  4  2
  subtype2 13 17
  subtype3  4  8
  subtype4 12  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2   13   17
  subtype3    4    8
  subtype4   12    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       13        4       12
  MALE          2       17        8        6

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype2 18  9
  subtype3 25 12
subtype2 subtype3 
      27       37 
subtype2 subtype3 
       9       12 
$subtype2
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       14.04        12.85        15.02        42.77         4.50        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48L TCGA-DX-A48O TCGA-FX-A3NJ TCGA-FX-A48G 
       44.45        39.35        24.26        27.22         0.10         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        4.14        12.62        21.37         8.94         3.22         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        31.76        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-LI-A67I TCGA-PC-A5DK 
       22.62         5.23        75.48 

$subtype3
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.23        76.37        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.78        60.30         8.55         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.01        23.08        70.49       108.10        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A48N TCGA-FX-A2QS 
       20.02        17.75        10.68        19.30        12.26         0.46 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W 
       26.89         4.54       143.41         5.88         1.05        11.70 
TCGA-MO-A47R 
        0.10 

subtype2 subtype3 
    0.07     0.10 
subtype2 subtype3 
  116.88   143.41 
subtype2 subtype3 
   15.02    20.02 
[1] "0.1 - 116.9 (15.0)" "0.1 - 143.4 (20.0)"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype3" "subtype2"
[1] "hr=" "1.2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype2 16 11
  subtype3 15 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2   16   11
  subtype3   15   22
        clus
vv       subtype2 subtype3
  FEMALE       16       15
  MALE         11       22

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  8  5
  subtype2 20 10
  subtype3 17  6
subtype1 subtype2 subtype3 
      13       30       23 
subtype1 subtype2 subtype3 
       5       10        6 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU 
       14.04        12.85        24.49        46.68         6.28        70.49 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-HB-A2OT TCGA-IE-A4EJ 
       17.10        15.02         4.50        10.68        26.89         3.22 
TCGA-LI-A67I 
        5.23 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.51        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.23        76.37        66.87        27.78        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.55         9.70        53.26        43.04         9.01        23.08 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-FX-A2QS 
      108.10        20.02        17.75        19.30        12.26         0.46 
TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W TCGA-MO-A47R 
        4.54       143.41         5.88         1.05        11.70         0.10 

$subtype3
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48L TCGA-DX-A48O 
       42.77        14.99        44.45        39.35        24.26        27.22 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
        0.10         0.07         0.07         4.14        12.62        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
       13.58        73.28        22.62         6.25        75.48 

subtype1 subtype2 subtype3 
    3.22     0.10     0.07 
subtype1 subtype2 subtype3 
   70.49   143.41   116.88 
subtype1 subtype2 subtype3 
   14.04    19.66    22.62 
[1] "3.2 - 70.5 (14.0)"  "0.1 - 143.4 (19.7)" "0.1 - 116.9 (22.6)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  4  9
  subtype2 13 17
  subtype3 16  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    9
  subtype2   13   17
  subtype3   16    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       13       16
  MALE          9       17        7

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype2 24 12
  subtype3 21  9
subtype2 subtype3 
      36       30 
subtype2 subtype3 
      12        9 
$subtype2
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.23        76.37        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.78        60.30         8.55         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.01        23.08        70.49       108.10        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A48N TCGA-FX-A2QS 
       20.02        17.75        10.68        19.30        12.26         0.46 
TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W TCGA-MO-A47R 
        4.54       143.41         5.88         1.05        11.70         0.10 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       14.04        12.85        15.02        42.77         4.50        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48L TCGA-DX-A48O TCGA-FX-A3NJ TCGA-FX-A3RE 
       44.45        39.35        24.26        27.22         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI 
        0.07        26.89         4.14        12.62        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        3.22         1.38        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-LI-A67I TCGA-PC-A5DK 
       13.58        73.28        22.62         6.25         5.23        75.48 

subtype2 subtype3 
    0.10     0.07 
subtype2 subtype3 
  143.41   116.88 
subtype2 subtype3 
  19.660   15.005 
[1] "0.1 - 143.4 (19.7)" "0.1 - 116.9 (15.0)"
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype2 14 22
  subtype3 19 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2   14   22
  subtype3   19   11
        clus
vv       subtype2 subtype3
  FEMALE       14       19
  MALE         22       11
> q(save="no")
