
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/LIHC-TP/8282707/LIHC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/8142945/LIHC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=LIHC-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=LIHC-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/LIHC-TP/8142945/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/8282707/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=157, in cluster file=205, common to both=155
[1]   8 155
[1] "CN_CNMF"
[1] 3
 1  2  3 
43 58 48 
 1  2  3 
43 58 48 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
42 43 69 
 1  2  3 
42 43 69 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
35 23 43 21 25 
 1  2  3  4  5 
35 23 43 21 25 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
25 25 55 42 
 1  2  3  4 
25 25 55 42 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
56 33 61 
 1  2  3 
56 33 61 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
15 67 26 42 
 1  2  3  4 
15 67 26 42 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
15 12 30 25 32 36 
 1  2  3  4  5  6 
15 12 30 25 32 36 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
13 69 68 
 1  2  3 
13 69 68 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "GLEASON_SCORE"                         
[19] "PSA_VALUE"                             
[20] "DAYS_TO_PSA"                           
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 155 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          849           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
          NA         1351          421            8          680          289 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
         120           16            2            5           NA           12 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 
          NA           NA           NA           NA           NA            3 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
           2            3            4         2425           NA           NA 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
          NA         3437           NA           79           NA          662 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
          NA           NA         2415         2017          602         2301 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
         204           NA           NA         1495          183          887 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
          NA           NA           NA           NA         1008          391 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
        2232           NA          428          455          433          561 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
         458           NA         1711           NA         1869         2849 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
          NA           NA           NA         2018          334           NA 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
         230          334           44          843         3071          408 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
         386          482          423          406            7            6 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
           6            6            6            6            6          570 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
         608          357          334           NA          303          363 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
          NA           NA          987           NA           NA            6 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
          NA           NA            4            1           10         1836 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
          12           37         1553         1636          860          935 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
        1779           NA          655          673          780          180 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
         594          585          447          364          302          243 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75C 
         133          236           NA          122           15          291 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
         155          433          265           NA          135 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=84,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
[3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
[5] "PATHOLOGY.M.STAGE"         "GENDER"                   
[7] "COMPLETENESS.OF.RESECTION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 155 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
62 40 44  9 
[1] "table(vv)"
vv
T1 T2 T3 T4 
62 40 44  9 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
62 40 44  9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
62 40 44  9 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 21 21
  subtype2 38 20
  subtype3 25 22
subtype1 subtype2 subtype3 
      42       58       47 
subtype1 subtype2 subtype3 
      21       20       22 
$subtype1
TCGA-BC-4072 TCGA-BC-A10U TCGA-CC-5258 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 
       48.99        27.52         0.07         0.13        79.73         7.33 
TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39V 
       90.71         6.71        12.95        45.11        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A7 
       55.69         5.62        19.76         7.66        17.59        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A73A TCGA-DD-A73D 
        0.36        14.07        39.78        61.45        10.98        10.98 
TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL 
      100.96        13.35         0.20        18.74         0.62         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A3CG 
       22.85        14.40        19.10        60.36         0.39        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-K7-A6G5 TCGA-MI-A75C TCGA-MI-A75I TCGA-O8-A75V 
       19.53         7.99         4.01         9.57         8.71         4.44 

$subtype2
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A69I TCGA-CC-5260 
       27.91        46.78        25.32        69.57         0.53         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A11D 
        3.39         3.32         0.10        37.78         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EK TCGA-DD-A3A2 
       79.40        66.31        19.79        75.65        18.35        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH 
       20.12       107.11        33.14        12.85        73.38        14.24 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       18.44        56.25        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG 
       66.35         9.30         7.56        27.72        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A3RK 
       13.91         0.23         0.20         0.20        19.99        11.93 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        8.12         0.13         0.33        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ 
       30.74        21.53        25.64         5.92        19.23        11.97 
TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-MI-A75E TCGA-NI-A4U2 
        4.37         1.02         5.10        58.88 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z 
       37.32        10.13        27.52         2.99        23.34         1.12 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A115 
        3.95         0.39         4.24         0.07         0.10        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33       113.00         2.60        21.76        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NN 
       29.16        25.81       102.74        30.61        15.06        29.56 
TCGA-DD-A73E TCGA-ED-A459 TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-EP-A2KA TCGA-EP-A2KB 
        1.45        13.41         0.20         0.20        11.74        10.98 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25X 
       32.45         0.20         6.38         0.03         1.22        58.49 
TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A6UC TCGA-LG-A6GG TCGA-MI-A75G 
       14.86        14.70         7.76         0.49        14.24 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  100.96   107.11   113.00 
subtype1 subtype2 subtype3 
  13.710   18.835   11.740 
[1] "0.1 - 101.0 (13.7)" "0.1 - 107.1 (18.8)" "0.0 - 113.0 (11.7)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[139] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[145] "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[139] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[145] "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [61] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
 [67] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [85] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[103] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[109] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[127] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[139] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[145] "subtype1" "subtype2" "subtype1"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      21        9         0          8          1          0        1
  subtype2      25       11         0         13          2          4        0
  subtype3      12       16         2          9          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D1V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 22 11 10  0
  subtype2 26 12 16  4
  subtype3 13 17 14  4
D1V4, multiclass
D1V5, binary
          cls
clus        0  1
  subtype1 26  1
  subtype2 44  1
  subtype3 27  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   44    1
  subtype3   27    1
   clus
vv  subtype1 subtype2 subtype3
  0       26       44       27
  1        1        1        1
          vv
clus       M0 M1 MX
  subtype1 31  1 11
  subtype2 47  1 10
  subtype3 37  1 10
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  9 34
  subtype2 28 30
  subtype3 21 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   34
  subtype2   28   30
  subtype3   21   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       28       21
  MALE         34       30       27
          vv
clus       R0 R1 R2 RX
  subtype1 33  5  1  3
  subtype2 50  1  0  3
  subtype3 39  5  0  4
D1V8, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 28 14
  subtype2 22 20
  subtype3 38 29
subtype1 subtype2 subtype3 
      42       42       67 
subtype1 subtype2 subtype3 
      14       20       29 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5258 TCGA-CC-5260 
       48.99        27.91        25.32        69.57         0.07         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A1E9 TCGA-DD-A1EC 
        3.39         3.32         0.10        37.78        90.71        19.79 
TCGA-DD-A1ED TCGA-DD-A1EL TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       75.65        13.64       107.11        33.14        12.85        73.38 
TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       14.24        56.25        93.67        12.26         0.30        80.75 
TCGA-DD-A73C TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
        7.56        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 
        0.20         0.20         0.20        11.93        14.40         0.13 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI TCGA-K7-A6G5 TCGA-MI-A75E 
       51.06        28.27        30.74         5.92         4.01         5.10 

$subtype2
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5259 
       37.32        10.13         2.99         5.03         3.95         0.16 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
        0.39         0.07         0.13        79.73        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X 
        7.33         0.46        12.95        49.15         6.02        55.69 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NN 
       17.59        20.12        13.78        30.61        21.70        29.56 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY 
       61.45         9.30       100.96        13.41         0.23         0.20 
TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       10.98        32.45         0.20         0.33        60.36         0.39 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-MI-A75C TCGA-O8-A75V 
       58.49        14.86        25.64        14.70         9.57         4.44 

$subtype3
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       46.78        27.52        27.52        23.34         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5263 
       13.84         0.26        22.36         9.50         0.53         4.24 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        0.10        83.57         2.60        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       66.31         6.71        45.11        29.16        18.35        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 
        5.62        19.76        25.81         7.66        70.06       102.74 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        14.07        14.96        18.44        15.06        39.78 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A7PZ 
       66.35        10.98        10.98         1.45        27.72         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QR 
       18.74        19.99        11.74         0.62         9.96        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z 
        8.12         6.38         0.03         1.22        53.79        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       22.13        19.53        19.23        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I 
        4.37         7.76         1.02         0.49        14.24         8.71 
TCGA-NI-A4U2 
       58.88 

subtype1 subtype2 subtype3 
    0.07     0.07     0.03 
subtype1 subtype2 subtype3 
  107.11   113.00   102.74 
subtype1 subtype2 subtype3 
  13.775   13.180   14.960 
[1] "0.1 - 107.1 (13.8)" "0.1 - 113.0 (13.2)" "0.0 - 102.7 (15.0)"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[139] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype2"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[139] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype2"
  [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [31] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [49] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
 [55] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [73] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [85] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[103] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[133] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[139] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype2"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      15        9         0         11          2          4        0
  subtype2      15       10         1          9          1          1        1
  subtype3      28       17         1         14          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         1
  subtype3         1         1
D2V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 16 10 13  3
  subtype2 15 11 14  3
  subtype3 30 19 17  3
D2V4, multiclass
D2V5, binary
          cls
clus        0  1
  subtype1 34  1
  subtype2 30  0
  subtype3 37  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    1
  subtype2   30    0
  subtype3   37    2
   clus
vv  subtype1 subtype2 subtype3
  0       34       30       37
  1        1        0        2
          vv
clus       M0 M1 MX
  subtype1 35  0  7
  subtype2 35  2  6
  subtype3 51  1 17
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1 19 23
  subtype2 20 23
  subtype3 22 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   23
  subtype2   20   23
  subtype3   22   47
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       19       20       22
  MALE         23       23       47
          vv
clus       R0 R1 R2 RX
  subtype1 34  2  0  3
  subtype2 35  4  1  3
  subtype3 57  5  0  5
D2V8, multiclass

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 18 17
  subtype2  9 13
  subtype3 24 18
  subtype4 14  7
  subtype5 18  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      35       22       42       21       25 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       13       18        7        7 
$subtype1
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 
       48.99        37.32        10.13         3.95         0.07         0.16 
TCGA-CC-5261 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EF 
        0.39         0.13        79.73       113.00         7.33        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A6 
       49.15        29.16        55.69        19.76        17.59       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73G TCGA-ED-A5KG 
       30.61        33.14        14.24        29.56       100.96        15.85 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B 
       13.35         0.23         0.20        11.74        10.98        32.45 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25X TCGA-G3-A25Y 
        0.20         0.13        60.36        58.49        14.86 

$subtype2
TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       27.91        27.52         2.99        44.42        13.84        22.36 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A1 
        4.24         3.32         0.10        45.11         5.62         7.66 
TCGA-DD-A3A7 TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-ED-A459 TCGA-FV-A3I1 TCGA-G3-A25S 
       13.78        12.26         0.30        13.41         8.12         1.22 
TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75I 
       11.97         1.02         0.49         8.71 

$subtype3
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 
       46.78        27.52        23.34         1.12         0.26         9.50 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        0.10        83.57         2.60         0.46        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI 
       66.31        18.35        70.06       102.74        21.70        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A 
       15.06        39.78        56.25        61.45        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        9.30         7.56        27.72        22.85        14.40        19.10 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
        6.38         0.33        53.79        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-MI-A75G TCGA-NI-A4U2 
        5.92        14.70         9.93         4.37        14.24        58.88 

$subtype4
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A3MA 
       25.32        69.57         5.03         2.86         3.39         0.07 
TCGA-DD-A114 TCGA-DD-A1EC TCGA-DD-A1EI TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NS 
       37.78        19.79         6.02        12.85        73.38        80.75 
TCGA-ED-A4XI TCGA-ED-A627 TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25V 
       12.69        13.91         9.96         0.03        51.06        28.27 
TCGA-K7-A6G5 TCGA-MI-A75E TCGA-O8-A75V 
        4.01         5.10         4.44 

$subtype5
TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
        0.53        53.33        79.40        75.65         6.71        13.64 
TCGA-DD-A39V TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP 
       21.14        20.12         0.36        14.07        14.96        93.67 
TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       10.98         1.45         0.20        18.74        19.99         0.62 
TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       11.93         0.39        19.53        19.23         7.99         7.76 
TCGA-MI-A75C 
        9.57 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.10     0.10     0.03     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
  113.00    45.11   102.74    80.75    93.67 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.850    8.415   20.315   12.690   13.640 
[1] "0.1 - 113.0 (15.8)" "0.1 - 45.1 (8.4)"   "0.1 - 102.7 (20.3)"
[4] "0.0 - 80.8 (12.7)"  "0.2 - 93.7 (13.6)" 
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype5" "subtype1" "subtype1" "subtype4" "subtype1"
 [25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype3" "subtype5" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype5"
 [43] "subtype3" "subtype4" "subtype5" "subtype5" "subtype1" "subtype2"
 [49] "subtype1" "subtype4" "subtype1" "subtype3" "subtype5" "subtype5"
 [55] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [61] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype1"
 [67] "subtype1" "subtype4" "subtype4" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype5" "subtype2" "subtype2" "subtype4" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5" "subtype3"
 [91] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
[103] "subtype1" "subtype5" "subtype4" "subtype5" "subtype3" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[115] "subtype4" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
[121] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype2"
[133] "subtype3" "subtype5" "subtype3" "subtype5" "subtype2" "subtype4"
[139] "subtype2" "subtype5" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype4"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype5" "subtype1" "subtype1" "subtype4" "subtype1"
 [25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype3" "subtype5" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype5"
 [43] "subtype3" "subtype4" "subtype5" "subtype5" "subtype1" "subtype2"
 [49] "subtype1" "subtype4" "subtype1" "subtype3" "subtype5" "subtype5"
 [55] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [61] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype1"
 [67] "subtype1" "subtype4" "subtype4" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype5" "subtype2" "subtype2" "subtype4" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5" "subtype3"
 [91] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
[103] "subtype1" "subtype5" "subtype4" "subtype5" "subtype3" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[115] "subtype4" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
[121] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype2"
[133] "subtype3" "subtype5" "subtype3" "subtype5" "subtype2" "subtype4"
[139] "subtype2" "subtype5" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype4"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype2" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [13] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype1" "subtype5" "subtype1" "subtype1" "subtype4" "subtype1"
 [25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype3"
 [31] "subtype1" "subtype1" "subtype4" "subtype3" "subtype5" "subtype1"
 [37] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype5"
 [43] "subtype3" "subtype4" "subtype5" "subtype5" "subtype1" "subtype2"
 [49] "subtype1" "subtype4" "subtype1" "subtype3" "subtype5" "subtype5"
 [55] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
 [61] "subtype5" "subtype3" "subtype1" "subtype2" "subtype5" "subtype1"
 [67] "subtype1" "subtype4" "subtype4" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype5" "subtype2" "subtype2" "subtype4" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5" "subtype3"
 [91] "subtype1" "subtype2" "subtype4" "subtype1" "subtype4" "subtype1"
 [97] "subtype1" "subtype1" "subtype5" "subtype5" "subtype5" "subtype1"
[103] "subtype1" "subtype5" "subtype4" "subtype5" "subtype3" "subtype3"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[115] "subtype4" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
[121] "subtype3" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype2"
[133] "subtype3" "subtype5" "subtype3" "subtype5" "subtype2" "subtype4"
[139] "subtype2" "subtype5" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype4"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8       12         1          6          1          3        1
  subtype2       5        7         0          7          1          0        0
  subtype3      23        5         1          9          0          0        0
  subtype4      10        3         0          3          0          3        0
  subtype5      11        7         0          6          1          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         1         1
  subtype4         0         0
  subtype5         0         0
D3V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  9 14 10  2
  subtype2  5  9  8  1
  subtype3 24  5 11  3
  subtype4 11  3  4  3
  subtype5 11  7  7  0
D3V4, multiclass
D3V5, binary
          cls
clus        0  1
  subtype1 22  2
  subtype2 14  0
  subtype3 29  1
  subtype4 14  0
  subtype5 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    2
  subtype2   14    0
  subtype3   29    1
  subtype4   14    0
  subtype5   16    0
          vv
clus       M0 M1 MX
  subtype1 28  2  5
  subtype2 17  0  6
  subtype3 33  1  9
  subtype4 15  0  6
  subtype5 20  0  5
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1 25 10
  subtype2  7 16
  subtype3 15 28
  subtype4  8 13
  subtype5  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   10
  subtype2    7   16
  subtype3   15   28
  subtype4    8   13
  subtype5    1   24
          vv
clus       R0 R1 R2 RX
  subtype1 29  3  1  2
  subtype2 15  4  0  3
  subtype3 37  3  0  3
  subtype4 16  1  0  2
  subtype5 23  0  0  0
D3V8, multiclass

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 15  9
  subtype2 18  7
  subtype3 27 27
  subtype4 23 19
subtype1 subtype2 subtype3 subtype4 
      24       25       54       42 
subtype1 subtype2 subtype3 subtype4 
       9        7       27       19 
$subtype1
TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5262 TCGA-DD-A1EG TCGA-DD-A1EI 
       46.78        25.32        69.57         3.39        45.11         6.02 
TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NO TCGA-DD-A4NS TCGA-ED-A4XI 
       20.12        12.85        73.38        61.45        80.75        12.69 
TCGA-ED-A627 TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25V 
       13.91         9.96        22.85         8.12         0.03        28.27 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A5SM TCGA-K7-A6G5 TCGA-MI-A75E TCGA-O8-A75V 
       21.53        22.13         4.37         4.01         5.10         4.44 

$subtype2
TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EJ 
        0.53        53.33        79.40        75.65         6.71        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NL 
       13.64        21.14         0.36        14.07        14.96        56.25 
TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
       93.67        10.98         1.45         0.20        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL 
        0.62        11.93         0.39        19.53        19.23         7.99 
TCGA-G3-A6UC 
        7.76 

$subtype3
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 
       48.99        27.91        37.32        10.13         2.99         5.03 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
        3.95         0.07         0.16         2.86         0.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.07         0.13        79.73        37.78 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39X 
      113.00         7.33        19.79        12.95        49.15        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
        5.62        19.76        17.59       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR 
       33.14        14.24        15.06        29.56        12.26         0.30 
TCGA-DD-A73G TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A2KA 
      100.96        15.85        13.35         0.23         0.20        11.74 
TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZP 
       10.98        14.40        32.45         0.20         0.13        60.36 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SJ TCGA-MI-A75C 
       51.06        58.49        14.86        25.64        11.97         9.57 

$subtype4
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
       27.52        27.52        23.34         1.12        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A 
        0.26        22.36         9.50         0.10        83.57         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A3A1 
        0.46        21.76        51.29        66.31        18.35         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NV 
       70.06       102.74        21.70        18.44        39.78        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A459 TCGA-FV-A2QR 
       10.98         9.30         7.56        27.72        13.41        19.10 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CI TCGA-G3-A5SI 
        6.38         0.33         1.22        53.79         5.92        14.70 
TCGA-G3-A5SK TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 
        9.93         1.02         0.49        14.24         8.71        58.88 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.20     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
   80.75    93.67   113.00   102.74 
subtype1 subtype2 subtype3 subtype4 
  17.015   14.070   13.565   14.470 
[1] "0.0 - 80.8 (17.0)"  "0.2 - 93.7 (14.1)"  "0.1 - 113.0 (13.6)"
[4] "0.1 - 102.7 (14.5)"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
 [13] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [31] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
 [37] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
 [43] "subtype4" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
 [73] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[115] "subtype1" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
[121] "subtype4" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[127] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[139] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype4"
[145] "subtype1"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
 [13] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [31] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
 [37] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
 [43] "subtype4" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
 [73] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[115] "subtype1" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
[121] "subtype4" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[127] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[139] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype4"
[145] "subtype1"
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
  [7] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
 [13] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [31] "subtype3" "subtype3" "subtype3" "subtype4" "subtype2" "subtype3"
 [37] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
 [43] "subtype4" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
 [55] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [61] "subtype1" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype1" "subtype4" "subtype2" "subtype2"
 [73] "subtype3" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
 [79] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype4" "subtype4" "subtype4" "subtype2" "subtype2" "subtype4"
 [91] "subtype3" "subtype4" "subtype1" "subtype3" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
[115] "subtype1" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
[121] "subtype4" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[127] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype3"
[133] "subtype4" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[139] "subtype4" "subtype3" "subtype1" "subtype4" "subtype4" "subtype4"
[145] "subtype1"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      14        4         0          2          0          2        0
  subtype2      11        7         0          5          1          1        0
  subtype3      14       15         1         14          2          3        1
  subtype4      18        8         1         10          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         0
  subtype3         0         1
  subtype4         0         1
D4V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 16  4  3  2
  subtype2 12  7  6  0
  subtype3 14 17 20  4
  subtype4 18 10 11  3
D4V4, multiclass
D4V5, binary
          cls
clus        0  1
  subtype1 16  1
  subtype2 15  1
  subtype3 37  1
  subtype4 27  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    1
  subtype2   15    1
  subtype3   37    1
  subtype4   27    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       16       15       37       27
  1        1        1        1        0
          vv
clus       M0 M1 MX
  subtype1 16  0  9
  subtype2 20  0  5
  subtype3 44  2  9
  subtype4 33  1  8
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1  6 19
  subtype2  2 23
  subtype3 29 26
  subtype4 19 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   19
  subtype2    2   23
  subtype3   29   26
  subtype4   19   23
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        2       29       19
  MALE         19       23       26       23
          vv
clus       R0 R1 R2 RX
  subtype1 20  2  0  1
  subtype2 23  0  0  0
  subtype3 43  5  1  5
  subtype4 34  4  0  4
D4V8, multiclass

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 36 19
  subtype2 14 18
  subtype3 36 24
subtype1 subtype2 subtype3 
      55       32       60 
subtype1 subtype2 subtype3 
      19       18       24 
$subtype1
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       48.99        37.32        27.52        25.32        69.57         5.03 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         0.16         2.86         0.39         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1ED TCGA-DD-A1EH 
        0.10         0.13        37.78         7.33        75.65        49.15 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND 
        6.02        55.69        25.81        30.61        12.85        73.38 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       14.24        18.44        56.25        29.56        61.45        93.67 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X 
       80.75        66.35       100.96        12.69        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KA TCGA-ES-A2HT TCGA-FV-A23B 
        0.20         0.20         0.20        11.74        14.40        32.45 
TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.20         0.39        51.06        28.27        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-K7-A6G5 TCGA-MI-A75E 
       21.53        25.64        11.97         4.37         4.01         5.10 
TCGA-O8-A75V 
        4.44 

$subtype2
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A69H TCGA-CC-5262 
       27.91        10.13        23.34         1.12         3.95         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EG 
        4.24         3.32        83.57        21.76        66.31        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 
       29.16        18.35        13.64         5.62         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A7PZ TCGA-EP-A3JL TCGA-FV-A2QR 
      102.74         1.45        27.72         0.20         9.96        19.10 
TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CI 
        8.12         0.03         1.22        30.74        22.13         5.92 
TCGA-LG-A6GG TCGA-MI-A75I 
        0.49         8.71 

$subtype3
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       46.78        27.52         2.99        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 
       22.36         9.50         0.53        79.73        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EE 
        2.60         0.46        51.29        79.40        19.79         6.71 
TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       12.95        21.14        19.76        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       13.78         0.36        33.14        21.70        14.07        14.96 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       12.26         0.30        10.98         9.30         7.56        10.98 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-EP-A12J 
       13.41        15.85         0.23         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A496 
       19.99        10.98         0.62        11.93        22.85         0.33 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SK 
       60.36        53.79        19.53        19.23        14.70         9.93 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-MI-A75C TCGA-MI-A75G TCGA-NI-A4U2 
        7.99         7.76         1.02         9.57        14.24        58.88 

subtype1 subtype2 subtype3 
    0.07     0.03     0.20 
subtype1 subtype2 subtype3 
  100.96   102.74   113.00 
subtype1 subtype2 subtype3 
  14.400   10.045   13.955 
[1] "0.1 - 101.0 (14.4)" "0.0 - 102.7 (10.0)" "0.2 - 113.0 (14.0)"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [49] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [73] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [97] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[145] "subtype2" "subtype3" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [49] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [73] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [97] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[145] "subtype2" "subtype3" "subtype1"
  [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
  [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
 [37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [43] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [49] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [67] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [73] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [97] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[109] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[115] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[127] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[133] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[139] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[145] "subtype2" "subtype3" "subtype1"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      21       10         1         14          1          3        1
  subtype2      13        6         1          5          1          2        0
  subtype3      22       19         0         14          2          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         1
  subtype3         0         0
D5V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 22 11 18  5
  subtype2 15  7  8  3
  subtype3 22 21 17  1
D5V4, multiclass
D5V5, binary
          cls
clus        0  1
  subtype1 39  0
  subtype2 22  2
  subtype3 37  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   22    2
  subtype3   37    1
   clus
vv  subtype1 subtype2 subtype3
  0       39       22       37
  1        0        2        1
          vv
clus       M0 M1 MX
  subtype1 45  2  9
  subtype2 24  1  8
  subtype3 49  0 12
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1 21 35
  subtype2 12 21
  subtype3 25 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   35
  subtype2   12   21
  subtype3   25   36
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       12       25
  MALE         35       21       36
          vv
clus       R0 R1 R2 RX
  subtype1 46  4  1  5
  subtype2 24  3  0  3
  subtype3 52  4  0  3
D5V8, multiclass

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  6  9
  subtype2 39 27
  subtype3 18  7
  subtype4 23 18
subtype1 subtype2 subtype3 subtype4 
      15       66       25       41 
subtype1 subtype2 subtype3 subtype4 
       9       27        7       18 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 
       48.99        27.91         1.12         3.39         3.32        83.57 
TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-ED-A7PZ TCGA-EP-A3JL 
       45.11        18.35        13.64        27.72         0.20         9.96 
TCGA-FV-A495 TCGA-G3-A25S TCGA-MI-A75I 
        0.03         1.22         8.71 

$subtype2
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A69H 
       37.32         2.99        25.32        69.57         5.03         3.95 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         0.16         2.86         0.39         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EC TCGA-DD-A1ED 
        0.13        37.78         7.33         0.46        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A0 
       12.95        49.15         6.02        29.16        55.69        25.81 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       17.59        20.12        30.61        33.14        12.85        73.38 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       21.70        14.24        18.44        56.25        29.56        61.45 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       80.75        66.35         9.30       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS 
        0.20         0.20         0.20        11.74        10.98        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V 
       14.40        32.45         0.20         0.39        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-K7-A6G5 TCGA-MI-A75E TCGA-O8-A75V 
       58.49        14.86        25.64         4.01         5.10         4.44 

$subtype3
TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5263 TCGA-DD-A116 
       27.52         0.26         9.50         0.53         4.24        53.33 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP 
       79.40         6.71        21.14         0.36        14.07        93.67 
TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73E TCGA-EP-A12J TCGA-EP-A26S TCGA-FV-A496 
        0.30        10.98         1.45        18.74        19.99         0.33 
TCGA-FV-A4ZP TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-MI-A75C 
       60.36        19.53        19.23         7.99         7.76         9.57 
TCGA-MI-A75G 
       14.24 

$subtype4
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 
       10.13        46.78        27.52        23.34        44.42        13.84 
TCGA-BC-A3KG TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
       22.36         0.10        79.73       113.00         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       51.29        66.31         5.62        19.76         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-DD-A73A 
      102.74       107.11        13.78        14.96        12.26        10.98 
TCGA-DD-A73C TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-G3-A25U 
        7.56         0.62        11.93        19.10         8.12        53.79 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SJ 
       30.74        21.53        22.13         5.92        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-NI-A4U2 
        9.93         4.37         1.02         0.49        58.88 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.26     0.10 
subtype1 subtype2 subtype3 subtype4 
   83.57   100.96    93.67   113.00 
subtype1 subtype2 subtype3 subtype4 
   9.960   14.075   10.980   14.960 
[1] "0.0 - 83.6 (10.0)"  "0.1 - 101.0 (14.1)" "0.3 - 93.7 (11.0)" 
[4] "0.1 - 113.0 (15.0)"
  [1] "subtype1" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype4"
 [31] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype4"
 [37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype3"
 [43] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [55] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype2" "subtype2" "subtype4" "subtype4" "subtype4" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype1"
[109] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[115] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[121] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype2"
[127] "subtype4" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
[133] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
[139] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype1" "subtype4" "subtype2"
  [1] "subtype1" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype4"
 [31] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype4"
 [37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype3"
 [43] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [55] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype2" "subtype2" "subtype4" "subtype4" "subtype4" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype1"
[109] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[115] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[121] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype2"
[127] "subtype4" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
[133] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
[139] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype1" "subtype4" "subtype2"
  [1] "subtype1" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
  [7] "subtype3" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
 [13] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype4"
 [31] "subtype2" "subtype4" "subtype2" "subtype1" "subtype3" "subtype4"
 [37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype3"
 [43] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [55] "subtype2" "subtype4" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype2" "subtype2" "subtype4" "subtype4" "subtype4" "subtype3"
 [67] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [73] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype4" "subtype3" "subtype2" "subtype2" "subtype4"
 [85] "subtype2" "subtype4" "subtype3" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype2" "subtype2" "subtype4" "subtype1"
[109] "subtype4" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[115] "subtype4" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
[121] "subtype2" "subtype4" "subtype2" "subtype4" "subtype2" "subtype2"
[127] "subtype4" "subtype4" "subtype2" "subtype4" "subtype3" "subtype3"
[133] "subtype4" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
[139] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype3"
[145] "subtype1" "subtype4" "subtype2"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       5        3         0          4          0          1        0
  subtype2      25       14         1         15          1          5        1
  subtype3      11        6         0          7          1          0        0
  subtype4      15       12         1          7          2          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         1
  subtype3         0         0
  subtype4         1         0
D6V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  5  4  4  2
  subtype2 27 16 19  5
  subtype3 11  7  8  0
  subtype4 16 12 12  2
D6V4, multiclass
D6V5, binary
          cls
clus        0  1
  subtype1 11  0
  subtype2 46  2
  subtype3 17  0
  subtype4 24  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    0
  subtype2   46    2
  subtype3   17    0
  subtype4   24    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       11       46       17       24
  1        0        2        0        1
          vv
clus       M0 M1 MX
  subtype1 10  1  4
  subtype2 54  2 11
  subtype3 22  0  4
  subtype4 32  0 10
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  5 10
  subtype2 31 36
  subtype3  4 22
  subtype4 18 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   10
  subtype2   31   36
  subtype3    4   22
  subtype4   18   24
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        5       31        4       18
  MALE         10       36       22       24
          vv
clus       R0 R1 R2 RX
  subtype1  9  3  0  0
  subtype2 57  3  1  6
  subtype3 20  3  0  2
  subtype4 36  2  0  3
D6V8, multiclass

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 10  4
  subtype2  4  8
  subtype3 16 14
  subtype4 17  8
  subtype5 17 13
  subtype6 22 14
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      14       12       30       25       30       36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        8       14        8       13       14 
$subtype1
TCGA-BC-4072 TCGA-BC-A10X TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 
       48.99        25.32         3.95         0.07         0.16         0.10 
TCGA-CC-A3MB TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EJ TCGA-ED-A66X TCGA-ED-A7PZ 
        0.10        66.31        75.65        29.16        13.35         0.20 
TCGA-FV-A23B TCGA-FV-A4ZQ 
       32.45         0.39 

$subtype2
TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A1EG 
       27.91         1.12         3.39         3.32        83.57        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S 
       18.35        13.64        27.72         9.96         0.03         1.22 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       37.32        46.78         5.03         2.86         0.39         4.24 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A3A3 
        0.07        79.73        19.79        12.95        49.15        17.59 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        33.14        21.70        14.24        29.56        61.45 
TCGA-DD-A4NR TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY 
        0.30       100.96        13.41        15.85         0.23         0.20 
TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A5SI 
       11.74         0.20        60.36        51.06        14.86        14.70 

$subtype4
TCGA-BC-A10R TCGA-BC-A110 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI 
       10.13        69.57         0.13        37.78         7.33         6.02 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NS TCGA-DD-A4NV 
       55.69        25.81        12.85        73.38        80.75        66.35 
TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ES-A2HT 
       12.69        13.91         0.20         0.20         0.20        14.40 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-K7-A6G5 TCGA-MI-A75E 
       28.27        58.49        25.64         4.37         4.01         5.10 
TCGA-O8-A75V 
        4.44 

$subtype5
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 
       27.52        27.52         2.99        23.34        44.42        13.84 
TCGA-BC-A3KG TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A39Y 
       22.36       113.00         2.60        21.76        51.29         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-DD-A73A 
        7.66       102.74        13.78        14.96        12.26        10.98 
TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-G3-A25U TCGA-G3-A25W 
        0.20        11.93        19.10         8.12        53.79        30.74 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A5SJ TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75I 
       21.53        22.13        11.97         1.02         0.49         8.71 

$subtype6
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1EA 
        0.26         9.50         0.53        53.33         0.46        79.40 
TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
        6.71        21.14        19.76        70.06        20.12       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A73B 
        0.36        14.07        18.44        56.25        93.67         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
        7.56        10.98         1.45        18.74        19.99        10.98 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        0.62        22.85         0.33         5.92        19.53        19.23 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-MI-A75C TCGA-MI-A75G TCGA-NI-A4U2 
        9.93         7.99         7.76         9.57        14.24        58.88 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.07     0.03     0.07     0.13     0.20     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   75.65    83.57   100.96    80.75   113.00   107.11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   8.650   11.800   15.355   12.850   14.400   12.525 
[1] "0.1 - 75.7 (8.7)"   "0.0 - 83.6 (11.8)"  "0.1 - 101.0 (15.4)"
[4] "0.1 - 80.8 (12.8)"  "0.2 - 113.0 (14.4)" "0.3 - 107.1 (12.5)"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype5"
  [7] "subtype5" "subtype5" "subtype1" "subtype5" "subtype2" "subtype4"
 [13] "subtype3" "subtype5" "subtype5" "subtype6" "subtype5" "subtype6"
 [19] "subtype1" "subtype6" "subtype1" "subtype1" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype6" "subtype5"
 [37] "subtype4" "subtype5" "subtype6" "subtype5" "subtype5" "subtype6"
 [43] "subtype1" "subtype3" "subtype1" "subtype6" "subtype3" "subtype2"
 [49] "subtype3" "subtype4" "subtype1" "subtype2" "subtype2" "subtype6"
 [55] "subtype4" "subtype5" "subtype6" "subtype4" "subtype5" "subtype6"
 [61] "subtype3" "subtype6" "subtype5" "subtype6" "subtype5" "subtype6"
 [67] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype6"
 [73] "subtype5" "subtype3" "subtype6" "subtype6" "subtype3" "subtype3"
 [79] "subtype6" "subtype5" "subtype3" "subtype4" "subtype4" "subtype5"
 [85] "subtype6" "subtype6" "subtype6" "subtype6" "subtype2" "subtype3"
 [91] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype3"
 [97] "subtype4" "subtype3" "subtype1" "subtype4" "subtype5" "subtype4"
[103] "subtype6" "subtype6" "subtype3" "subtype6" "subtype6" "subtype2"
[109] "subtype5" "subtype6" "subtype4" "subtype1" "subtype5" "subtype3"
[115] "subtype5" "subtype2" "subtype6" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype5" "subtype4" "subtype5" "subtype4" "subtype3"
[127] "subtype5" "subtype5" "subtype4" "subtype6" "subtype6" "subtype6"
[133] "subtype3" "subtype5" "subtype6" "subtype6" "subtype4" "subtype6"
[139] "subtype5" "subtype4" "subtype5" "subtype6" "subtype4" "subtype6"
[145] "subtype5" "subtype6" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype5"
  [7] "subtype5" "subtype5" "subtype1" "subtype5" "subtype2" "subtype4"
 [13] "subtype3" "subtype5" "subtype5" "subtype6" "subtype5" "subtype6"
 [19] "subtype1" "subtype6" "subtype1" "subtype1" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype6" "subtype5"
 [37] "subtype4" "subtype5" "subtype6" "subtype5" "subtype5" "subtype6"
 [43] "subtype1" "subtype3" "subtype1" "subtype6" "subtype3" "subtype2"
 [49] "subtype3" "subtype4" "subtype1" "subtype2" "subtype2" "subtype6"
 [55] "subtype4" "subtype5" "subtype6" "subtype4" "subtype5" "subtype6"
 [61] "subtype3" "subtype6" "subtype5" "subtype6" "subtype5" "subtype6"
 [67] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype6"
 [73] "subtype5" "subtype3" "subtype6" "subtype6" "subtype3" "subtype3"
 [79] "subtype6" "subtype5" "subtype3" "subtype4" "subtype4" "subtype5"
 [85] "subtype6" "subtype6" "subtype6" "subtype6" "subtype2" "subtype3"
 [91] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype3"
 [97] "subtype4" "subtype3" "subtype1" "subtype4" "subtype5" "subtype4"
[103] "subtype6" "subtype6" "subtype3" "subtype6" "subtype6" "subtype2"
[109] "subtype5" "subtype6" "subtype4" "subtype1" "subtype5" "subtype3"
[115] "subtype5" "subtype2" "subtype6" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype5" "subtype4" "subtype5" "subtype4" "subtype3"
[127] "subtype5" "subtype5" "subtype4" "subtype6" "subtype6" "subtype6"
[133] "subtype3" "subtype5" "subtype6" "subtype6" "subtype4" "subtype6"
[139] "subtype5" "subtype4" "subtype5" "subtype6" "subtype4" "subtype6"
[145] "subtype5" "subtype6" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype5"
  [7] "subtype5" "subtype5" "subtype1" "subtype5" "subtype2" "subtype4"
 [13] "subtype3" "subtype5" "subtype5" "subtype6" "subtype5" "subtype6"
 [19] "subtype1" "subtype6" "subtype1" "subtype1" "subtype3" "subtype3"
 [25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
 [31] "subtype4" "subtype3" "subtype4" "subtype2" "subtype6" "subtype5"
 [37] "subtype4" "subtype5" "subtype6" "subtype5" "subtype5" "subtype6"
 [43] "subtype1" "subtype3" "subtype1" "subtype6" "subtype3" "subtype2"
 [49] "subtype3" "subtype4" "subtype1" "subtype2" "subtype2" "subtype6"
 [55] "subtype4" "subtype5" "subtype6" "subtype4" "subtype5" "subtype6"
 [61] "subtype3" "subtype6" "subtype5" "subtype6" "subtype5" "subtype6"
 [67] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype6"
 [73] "subtype5" "subtype3" "subtype6" "subtype6" "subtype3" "subtype3"
 [79] "subtype6" "subtype5" "subtype3" "subtype4" "subtype4" "subtype5"
 [85] "subtype6" "subtype6" "subtype6" "subtype6" "subtype2" "subtype3"
 [91] "subtype3" "subtype4" "subtype3" "subtype4" "subtype1" "subtype3"
 [97] "subtype4" "subtype3" "subtype1" "subtype4" "subtype5" "subtype4"
[103] "subtype6" "subtype6" "subtype3" "subtype6" "subtype6" "subtype2"
[109] "subtype5" "subtype6" "subtype4" "subtype1" "subtype5" "subtype3"
[115] "subtype5" "subtype2" "subtype6" "subtype3" "subtype1" "subtype2"
[121] "subtype3" "subtype5" "subtype4" "subtype5" "subtype4" "subtype3"
[127] "subtype5" "subtype5" "subtype4" "subtype6" "subtype6" "subtype6"
[133] "subtype3" "subtype5" "subtype6" "subtype6" "subtype4" "subtype6"
[139] "subtype5" "subtype4" "subtype5" "subtype6" "subtype4" "subtype6"
[145] "subtype5" "subtype6" "subtype4"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       3        4         0          6          0          2        0
  subtype2       5        2         0          3          0          1        0
  subtype3       8        7         1          7          1          2        0
  subtype4      11        5         0          5          0          1        1
  subtype5      10        8         1          5          2          0        0
  subtype6      19        9         0          7          1          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         1
  subtype3         0         1
  subtype4         0         0
  subtype5         1         0
  subtype6         0         0
D7V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  4  4  6  1
  subtype2  5  2  3  2
  subtype3  8  9 11  2
  subtype4 12  5  7  1
  subtype5 11 10  8  3
  subtype6 19  9  8  0
D7V4, multiclass
D7V5, binary
          cls
clus        0  1
  subtype1 11  1
  subtype2 10  0
  subtype3 22  1
  subtype4 15  0
  subtype5 18  1
  subtype6 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    1
  subtype2   10    0
  subtype3   22    1
  subtype4   15    0
  subtype5   18    1
  subtype6   22    0
          vv
clus       M0 M1 MX
  subtype1 14  0  1
  subtype2  8  1  3
  subtype3 25  1  4
  subtype4 19  1  5
  subtype5 23  0  9
  subtype6 29  0  7
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1  7  8
  subtype2  4  8
  subtype3 19 11
  subtype4  7 18
  subtype5 12 20
  subtype6  9 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    8
  subtype2    4    8
  subtype3   19   11
  subtype4    7   18
  subtype5   12   20
  subtype6    9   27
          vv
clus       R0 R1 R2 RX
  subtype1 12  1  0  2
  subtype2  7  2  0  0
  subtype3 25  2  0  3
  subtype4 22  1  1  1
  subtype5 23  4  0  4
  subtype6 33  1  0  1
D7V8, multiclass

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  5  8
  subtype2 42 25
  subtype3 39 28
subtype1 subtype2 subtype3 
      13       67       67 
subtype1 subtype2 subtype3 
       8       25       28 
$subtype1
TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A1EG 
       27.91         1.12         3.39         3.32        83.57        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S 
       18.35        13.64        27.72         9.96         0.03         1.22 
TCGA-MI-A75I 
        8.71 

$subtype2
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A216 
       10.13        46.78        27.52        27.52        23.34        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5263 
       13.84         0.26        22.36         9.50         0.53         4.24 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       79.73        53.33       113.00         2.60        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       79.40        66.31         6.71        21.14         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
        7.66        70.06       102.74       107.11        13.78         0.36 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A 
       14.07        14.96        93.67        12.26         0.30        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        7.56        10.98         1.45         0.20        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP 
        0.62        11.93        19.10         8.12         0.33        60.36 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       53.79        28.27        30.74        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G 
        4.37         7.76         1.02         0.49         9.57        14.24 
TCGA-NI-A4U2 
       58.88 

$subtype3
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       48.99        37.32         2.99        25.32        69.57         5.03 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 
        3.95         0.07         0.16         2.86         0.39         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B 
        0.07         0.10         0.13        37.78         7.33         0.46 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69        25.81        17.59        20.12        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL 
       12.85        73.38        21.70        14.24        18.44        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73G 
       29.56        61.45        80.75        66.35         9.30       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20         0.20        11.74 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ 
       10.98        22.85        14.40        32.45         0.20         0.39 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-K7-A6G5 TCGA-MI-A75E 
       51.06        58.49        14.86        25.64         4.01         5.10 
TCGA-O8-A75V 
        4.44 

subtype1 subtype2 subtype3 
    0.03     0.20     0.07 
subtype1 subtype2 subtype3 
   83.57   113.00   100.96 
subtype1 subtype2 subtype3 
    9.96    14.24    13.91 
[1] "0.0 - 83.6 (10.0)"  "0.2 - 113.0 (14.2)" "0.1 - 101.0 (13.9)"
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[115] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[145] "subtype1" "subtype2" "subtype3"
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[115] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[145] "subtype1" "subtype2" "subtype3"
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [37] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [55] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[115] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[145] "subtype1" "subtype2" "subtype3"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       5        2         0          3          0          1        0
  subtype2      27       19         1         13          3          0        0
  subtype3      24       14         1         17          1          5        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         1
D8V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  5  3  3  2
  subtype2 28 20 19  2
  subtype3 26 16 21  5
D8V4, multiclass
D8V5, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 42  1
  subtype3 46  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   42    1
  subtype3   46    2
   clus
vv  subtype1 subtype2 subtype3
  0       10       42       46
  1        0        1        2
          vv
clus       M0 M1 MX
  subtype1  8  1  4
  subtype2 55  0 14
  subtype3 55  2 11
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1  4  9
  subtype2 23 46
  subtype3 31 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    9
  subtype2   23   46
  subtype3   31   37
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4       23       31
  MALE          9       46       37
          vv
clus       R0 R1 R2 RX
  subtype1  8  2  0  0
  subtype2 57  5  0  5
  subtype3 57  4  1  6
D8V8, multiclass
> q(save="no")
