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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/6159718/SARC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/6154784/SARC-TP.merged_data.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/Append_Data/SARC-TP/6154784/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/6159718/SARC-TP.mergedcluster.txt"

nPatients in clinical file=82, in cluster file=127, common to both=82
[1]  8 82
[1] "CN_CNMF"
[1] 3
 1  2  3 
29 30 23 
 1  2  3 
29 30 23 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
24 25 33 
 1  2  3 
24 25 33 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
30 21 21 
 1  2  3 
30 21 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
29 41  2 
 1  2 
29 41 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
 6 31 12 19 
 1  2  3  4 
 6 31 12 19 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 2 28 38 
 2  3 
28 38 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
13 31 24 
 1  2  3 
13 31 24 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 2  3 
37 31 
 2  3 
37 31 
[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 82 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-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1951           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
         828          455          805         2212          763          349 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
        1669          328          495           63          223           51 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
          NA           14            3            2            2          818 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
          NA          126           NA          650          272           98 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
          42           NA          966           NA         4362         3555 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
          NA         2229           NA          688          190           NA 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MO-A47R TCGA-PC-A5DK 
         356          159            3         2296 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=56,	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=8,	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 82 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 19 10
  subtype2 21  9
  subtype3 18  5
subtype1 subtype2 subtype3 
      29       30       23 
subtype1 subtype2 subtype3 
      10        9        5 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        24.49        18.51        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 
       29.85         5.23        76.37        66.87         6.28        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
        8.55         9.70         9.01        23.08        70.49       108.10 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A48N TCGA-DX-A6BF 
       17.10        20.02        15.02        17.75        12.26         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IW-A3M5 
        7.33         1.68         0.46         4.54         5.88 

$subtype2
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3U9 
       27.19        12.85        46.68        74.66        42.77        14.99 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R 
       28.80        34.88        64.14        24.26        27.22        26.47 
TCGA-DX-A6BA TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
       54.87         0.07         0.07        26.89         4.14        12.62 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3KA 
       21.37         8.94         3.22        25.22        28.21        13.58 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MO-A47R 
       22.62         6.25         1.05        11.70         5.23         0.10 

$subtype3
TCGA-DX-A23Z TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       27.78        53.26        43.04         4.50        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       39.35         9.73        19.30        14.96        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-IE-A4EK 
       11.47        10.78        16.27        16.18         0.10         1.38 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-PC-A5DK 
       31.76       143.41       116.88        73.28        75.48 

subtype1 subtype2 subtype3 
    0.46     0.07     0.10 
subtype1 subtype2 subtype3 
  108.10    74.66   143.41 
subtype1 subtype2 subtype3 
  15.020   21.995   25.080 
[1] "0.5 - 108.1 (15.0)" "0.1 - 74.7 (22.0)"  "0.1 - 143.4 (25.1)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
[61] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  8 21
  subtype2 23  7
  subtype3  9 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   21
  subtype2   23    7
  subtype3    9   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       23        9
  MALE         21        7       14

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16  8
  subtype2 17  8
  subtype3 25  8
subtype1 subtype2 subtype3 
      24       25       33 
subtype1 subtype2 subtype3 
       8        8        8 
$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-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       43.04         9.01        70.49        15.02        17.75         4.50 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-HB-A2OT TCGA-IE-A4EJ 
       16.27         7.33         1.68        16.18        26.89         3.22 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ 
        2.04        18.51        46.68        74.66         6.28         8.55 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA 
        9.70        23.08       108.10        17.10        20.02        10.68 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BF TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV 
       19.30        12.26         2.07         0.46         0.07         4.54 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I 
      143.41        13.58         5.88         1.05        11.70         5.23 
TCGA-MO-A47R 
        0.10 

$subtype3
TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       12.85        42.77        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88        64.14         9.73        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10         0.07         4.14        12.62        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 
        1.38        25.22        31.76        28.21       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
       22.62         6.25        75.48 

subtype1 subtype2 subtype3 
    1.68     0.07     0.07 
subtype1 subtype2 subtype3 
   76.37   143.41   116.88 
subtype1 subtype2 subtype3 
   25.69    10.68    25.08 
[1] "1.7 - 76.4 (25.7)"  "0.1 - 143.4 (10.7)" "0.1 - 116.9 (25.1)"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "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" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "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" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "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" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[79] "subtype2" "subtype2" "subtype2" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  9 15
  subtype2 12 13
  subtype3 19 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   15
  subtype2   12   13
  subtype3   19   14
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       12       19
  MALE         15       13       14

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 19 11
  subtype2 15  6
  subtype3 15  6
subtype1 subtype2 subtype3 
      30       21       21 
subtype1 subtype2 subtype3 
      11        6        6 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        24.49        18.51        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.44        31.56         5.23        76.37        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.78         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-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BH TCGA-IE-A4EJ TCGA-LI-A67I 
        4.50        10.68        12.26         1.68         3.22         5.23 

$subtype2
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3UB TCGA-FX-A2QS TCGA-FX-A3RE 
       12.85        74.66         8.55        44.45         0.46         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K7 
        0.07        26.89         4.54        21.37        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.88        22.62         6.25 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-MO-A47R 
        1.05        11.70         0.10 

$subtype3
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       42.77        14.99        39.35        28.80        34.88        64.14 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A6BA TCGA-FX-A3NJ TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EI TCGA-IE-A4EK 
       54.87         0.10         4.14        12.62         8.94         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-PC-A5DK 
       25.22        31.76        75.48 

subtype1 subtype2 subtype3 
    1.68     0.07     0.10 
subtype1 subtype2 subtype3 
  108.10   143.41    75.48 
subtype1 subtype2 subtype3 
   18.13    12.85    26.47 
[1] "1.7 - 108.1 (18.1)" "0.1 - 143.4 (12.8)" "0.1 - 75.5 (26.5)" 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  9 21
  subtype2 17  4
  subtype3 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   21
  subtype2   17    4
  subtype3   11   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       17       11
  MALE         21        4       10

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 21  8
  subtype2 27 14
subtype1 subtype2 
      29       41 
subtype1 subtype2 
       8       14 
$subtype1
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       42.77        14.99        39.35        28.80        34.88        64.14 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A6BA TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       54.87         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-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
       13.58        73.28        22.62         6.25        75.48 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.51 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        74.66         5.23        76.37 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        27.78         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-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BH 
       20.02        15.02        17.75        10.68        12.26         1.68 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EJ TCGA-IS-A3K7 
        0.46         0.07        26.89         4.54         3.22       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MO-A47R 
        5.88         1.05        11.70         5.23         0.10 

subtype1 subtype2 
    0.07     0.07 
subtype1 subtype2 
  116.88   143.41 
subtype1 subtype2 
   25.22    15.02 
[1] "0.1 - 116.9 (25.2)" "0.1 - 143.4 (15.0)"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "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" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "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" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "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" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[67] "subtype2" "subtype2" "subtype2" "subtype1"
[1] "hr=" "1.5"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 19 10
  subtype2 18 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   10
  subtype2   18   23
        clus
vv       subtype1 subtype2
  FEMALE       19       18
  MALE         10       23

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  3  3
  subtype2 21 10
  subtype3  8  4
  subtype4 15  4
subtype1 subtype2 subtype3 subtype4 
       6       31       12       19 
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-DX-A6BF 
      108.10        20.02        17.75        19.30        12.26         2.07 
TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
        0.46         4.54       143.41         5.88         6.25         1.05 
TCGA-KF-A41W 
       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-DX-A6BA 
       42.77        14.99        39.35        24.26        27.22        54.87 
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-A3K8 TCGA-IW-A3M4 
        8.94         1.38        25.22        31.76       116.88        73.28 
TCGA-PC-A5DK 
       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   19.300   23.555   24.260 
[1] "0.1 - 14.0 (8.0)"   "0.5 - 143.4 (19.3)" "4.5 - 70.5 (23.6)" 
[4] "0.1 - 116.9 (24.3)"
 [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" "subtype4" "subtype2" "subtype2"
[43] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype4"
[55] "subtype4" "subtype3" "subtype2" "subtype4" "subtype3" "subtype4"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "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" "subtype4" "subtype2" "subtype2"
[43] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype4"
[55] "subtype4" "subtype3" "subtype2" "subtype4" "subtype3" "subtype4"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "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" "subtype4" "subtype2" "subtype2"
[43] "subtype4" "subtype4" "subtype4" "subtype3" "subtype2" "subtype4"
[49] "subtype4" "subtype4" "subtype4" "subtype1" "subtype4" "subtype4"
[55] "subtype4" "subtype3" "subtype2" "subtype4" "subtype3" "subtype4"
[61] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype1" "subtype4"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  4  2
  subtype2 14 17
  subtype3  4  8
  subtype4 13  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2   14   17
  subtype3    4    8
  subtype4   13    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       14        4       13
  MALE          2       17        8        6

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype2 19  9
  subtype3 26 12
subtype2 subtype3 
      28       38 
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-DX-A6BA TCGA-FX-A3NJ 
       44.45        39.35        24.26        27.22        54.87         0.10 
TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.07         4.14        12.62        21.37         8.94         3.22 
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-LI-A67I TCGA-PC-A5DK 
       73.28        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-DX-A6BF 
       20.02        17.75        10.68        19.30        12.26         2.07 
TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF 
        0.46        26.89         4.54       143.41         5.88         1.05 
TCGA-KF-A41W TCGA-MO-A47R 
       11.70         0.10 

subtype2 subtype3 
    0.07     0.10 
subtype2 subtype3 
  116.88   143.41 
subtype2 subtype3 
  18.195   19.660 
[1] "0.1 - 116.9 (18.2)" "0.1 - 143.4 (19.7)"
 [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" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype3" "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" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype3" "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" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype2 17 11
  subtype3 16 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2   17   11
  subtype3   16   22
        clus
vv       subtype2 subtype3
  FEMALE       17       16
  MALE         11       22

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  8  5
  subtype2 21 10
  subtype3 18  6
subtype1 subtype2 subtype3 
      13       31       24 
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-DX-A6BF 
      108.10        20.02        17.75        19.30        12.26         2.07 
TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W 
        0.46         4.54       143.41         5.88         1.05        11.70 
TCGA-MO-A47R 
        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-DX-A6BA TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 
       54.87         0.10         0.07         0.07         4.14        12.62 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37         8.94         1.38        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-PC-A5DK 
      116.88        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    19.30    23.44 
[1] "3.2 - 70.5 (14.0)"  "0.1 - 143.4 (19.3)" "0.1 - 116.9 (23.4)"
 [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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[67] "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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[67] "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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[67] "subtype2" "subtype3"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  4  9
  subtype2 14 17
  subtype3 17  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    9
  subtype2   14   17
  subtype3   17    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       14       17
  MALE          9       17        7

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype2 25 12
  subtype3 22  9
subtype2 subtype3 
      37       31 
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-DX-A6BF 
       20.02        17.75        10.68        19.30        12.26         2.07 
TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W 
        0.46         4.54       143.41         5.88         1.05        11.70 
TCGA-MO-A47R 
        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-DX-A6BA TCGA-FX-A3NJ 
       44.45        39.35        24.26        27.22        54.87         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
        0.07         0.07        26.89         4.14        12.62        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-LI-A67I 
      116.88        13.58        73.28        22.62         6.25         5.23 
TCGA-PC-A5DK 
       75.48 

subtype2 subtype3 
    0.10     0.07 
subtype2 subtype3 
  143.41   116.88 
subtype2 subtype3 
   19.30    15.02 
[1] "0.1 - 143.4 (19.3)" "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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[67] "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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[67] "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" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[61] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[67] "subtype2" "subtype3"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype2 15 22
  subtype3 20 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2   15   22
  subtype3   20   11
        clus
vv       subtype2 subtype3
  FEMALE       15       20
  MALE         22       11
> q(save="no")
