
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/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LIHC-TP/4430497/LIHC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LIHC-TP/4397111/LIHC-TP.clin.merged.picked.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/GDAC_clinicalDataPicker/LIHC-TP/4397111/LIHC-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LIHC-TP/4430497/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=127, in cluster file=141, common to both=119
[1]   8 119
[1] "CN_CNMF"
[1] 3
 1  2  3 
37 34 46 
 1  2  3 
37 34 46 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
26 34 50 
 1  2  3 
26 34 50 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
30 15 21 22 27 
 1  2  3  4  5 
30 15 21 22 27 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
43 51 21 
 1  2  3 
43 51 21 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
12 10 28 25 39 
 1  2  3  4  5 
12 10 28 25 39 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 9 59 46 
 1  2  3 
 9 59 46 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
26 53 35 
 1  2  3 
26 53 35 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
39 10 65 
 1  2  3 
39 10 65 
[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] "BATCHNUMBER"                           

Input Data has 18 rows and 119 columns.

[1] "Batch" "18"   
[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          420            8          498          289 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
           2            5           NA           NA           NA           NA 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
          NA           NA           NA            3            2            3 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
           4         2425           NA           NA           NA         3436 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          662           NA           NA 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        2414         2017          601         2301          203           NA 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        1495          183          887           NA           NA           NA 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
        1008         2232           NA          428          454          433 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
         328          458           NA         1711           NA         1869 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
        2849           NA            7            6          330          236 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
         357           60           19           97           13           NA 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
          NA          987           NA           NA            6           NA 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
          NA            4            1           10         1836           12 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
          37         1552         1636          860          934         1779 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
          NA          655          673          780          179          594 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
         585          364          302          243          133 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=63,	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=17,	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=2,	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:'BATCH.NUMBER':	nDistinctValues=10,	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 119 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=49, 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 
48 28 35  7 
[1] "table(vv)"
vv
T1 T2 T3 T4 
48 28 35  7 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
48 28 35  7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
48 28 35  7 
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 18 17
  subtype2 22 12
  subtype3 21 24
subtype1 subtype2 subtype3 
      35       34       45 
subtype1 subtype2 subtype3 
      17       12       24 
$subtype1
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A216 TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3MC 
       48.99        46.78        44.42         0.07         3.32         0.13 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF 
       79.73       112.96         7.33        90.67         6.67        12.95 
TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A8 
        6.02        21.14        55.66        19.73        17.59         0.36 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NK TCGA-DD-A4NO TCGA-EP-A12J TCGA-EP-A26S 
       14.07        14.93        39.75        61.45        10.85         7.76 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3R2 
        0.62         3.19         0.43        23.01        14.40         6.35 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       60.36         0.39        22.13        19.53         7.99 

$subtype2
TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A3M9 
       27.91        25.32        69.57         2.86         3.39         0.10 
TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       37.74         0.46        51.25        79.36        19.76        75.65 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4ND TCGA-DD-A4NH 
        7.66        70.06        20.12       107.11        73.38        14.24 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A2KB 
       10.78        56.25        93.67        12.26         0.20         1.97 
TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI 
        0.13        51.02        53.79        28.27        25.64         5.88 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SM 
       19.23        11.97         9.93         4.37 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y 
       37.32        10.13        27.52        27.52         2.99        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12         5.03        13.81         0.26        16.37         9.50 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 
        3.02         4.24         0.07         0.10        83.57        53.29 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
        2.60        21.76        66.31        49.15        29.16        13.64 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
        5.59        25.81       102.74        13.78        30.58        33.14 
TCGA-DD-A4NE TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-ED-A459 TCGA-EP-A2KA TCGA-FV-A23B 
       21.67        15.06        29.56         0.23        11.74        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25W 
       19.07         0.20         0.03         0.33         1.22        30.71 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       58.49        14.86        21.53 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  112.96   107.11   102.74 
subtype1 subtype2 subtype3 
   14.40    19.94    15.06 
[1] "0.1 - 113.0 (14.4)" "0.1 - 107.1 (19.9)" "0.0 - 102.7 (15.1)"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[109] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[109] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
  [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [13] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [49] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [61] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [67] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [73] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [91] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [97] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[109] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      16        8         0         10          0          0        1
  subtype2      16        7         0          6          1          2        0
  subtype3      13       10         2          9          2          2        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         0
  subtype3         0         1
D1V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 17  8 12  0
  subtype2 17  7  7  2
  subtype3 14 13 15  4
D1V4, multiclass
D1V5, binary
          cls
clus        0  1
  subtype1 20  1
  subtype2 26  0
  subtype3 28  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   26    0
  subtype3   28    2
   clus
vv  subtype1 subtype2 subtype3
  0       20       26       28
  1        1        0        2
          vv
clus       M0 M1 MX
  subtype1 25  1 11
  subtype2 29  0  5
  subtype3 36  1  9
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  9 28
  subtype2 14 20
  subtype3 21 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   28
  subtype2   14   20
  subtype3   21   25
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       14       21
  MALE         28       20       25
          vv
clus       R0 R1 R2 RX
  subtype1 28  3  1  1
  subtype2 30  1  0  2
  subtype3 35  6  0  5
D1V8, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 15 11
  subtype2 18 15
  subtype3 24 23
subtype1 subtype2 subtype3 
      26       33       47 
subtype1 subtype2 subtype3 
      11       15       23 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5258 
       48.99        27.91        37.32        25.32        69.57         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A1E9 
        2.86         3.39         3.32         0.10        37.74        90.67 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH 
       19.76        75.65       107.11        33.14        73.38        14.24 
TCGA-ED-A5KG TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25V 
        0.20         0.43        14.40         0.13        51.02        28.27 
TCGA-G3-A25W TCGA-G3-A3CI 
       30.71         5.88 

$subtype2
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-A3MA 
       10.13         2.99         5.03         0.16         3.02         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.13        79.73        53.29       112.96         7.33         0.46 
TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A3 
       66.31        12.95        49.15         6.02        55.66        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-ED-A459 TCGA-EP-A12J 
       20.12        13.78        30.58        21.67         0.23        10.85 
TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        1.97        32.45         0.20         0.33        60.36         0.39 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       58.49        14.86        25.64 

$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-CC-5263 TCGA-CC-A3MB TCGA-DD-A115 
       13.81         0.26        16.37         4.24         0.10        83.57 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EJ 
        2.60        21.76        51.25        79.36         6.67        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14         5.59        19.73        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI 
       70.06       102.74         0.36        14.07        14.93        10.78 
TCGA-DD-A4NJ TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QR 
       15.06         7.76        11.74         0.62         3.19        19.07 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG 
        6.35         0.03         1.22        53.79        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        11.97         9.93         7.99 

subtype1 subtype2 subtype3 
    0.07     0.07     0.03 
subtype1 subtype2 subtype3 
  107.11   112.96   102.74 
subtype1 subtype2 subtype3 
  26.615   12.950   14.930 
[1] "0.1 - 107.1 (26.6)" "0.1 - 113.0 (12.9)" "0.0 - 102.7 (14.9)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [61] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [61] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [19] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
 [25] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
 [43] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [61] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
 [73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [79] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [85] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [97] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype3"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8        4         0          6          2          3        0
  subtype2      11        7         1          8          1          1        1
  subtype3      21       12         1         10          0          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         1
  subtype3         1         0
D2V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  9  6  8  2
  subtype2 11  7 13  3
  subtype3 23 13 12  2
D2V4, multiclass
D2V5, binary
          cls
clus        0  1
  subtype1 19  1
  subtype2 24  0
  subtype3 27  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    1
  subtype2   24    0
  subtype3   27    2
   clus
vv  subtype1 subtype2 subtype3
  0       19       24       27
  1        1        0        2
          vv
clus       M0 M1 MX
  subtype1 19  0  7
  subtype2 27  2  5
  subtype3 38  0 12
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1 14 12
  subtype2 15 19
  subtype3 15 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   12
  subtype2   15   19
  subtype3   15   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       15       15
  MALE         12       19       35
          vv
clus       R0 R1 R2 RX
  subtype1 18  3  0  2
  subtype2 28  2  1  3
  subtype3 40  4  0  4
D2V8, multiclass

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 16 14
  subtype2  7  6
  subtype3 12  8
  subtype4 12 10
  subtype5 14 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       13       20       22       27 
subtype1 subtype2 subtype3 subtype4 subtype5 
      14        6        8       10       13 
$subtype1
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-5260 
       48.99        37.32        10.13         5.03         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        3.02         4.24         0.10         0.07        79.73        37.74 
TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X 
      112.96        19.76        12.95        49.15         6.02        55.66 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NN 
      107.11        30.58        33.14        73.38        14.24        29.56 
TCGA-ED-A5KG TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
        0.20         0.20         0.13        51.02        58.49        14.86 

$subtype2
TCGA-BC-4073 TCGA-BC-A10W TCGA-CC-5259 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A39Y 
       27.91         2.99         0.16         3.32         0.13         5.59 
TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NQ TCGA-ED-A459 TCGA-EP-A2KA TCGA-FV-A4ZP 
        7.66        13.78        12.26         0.23        11.74        60.36 
TCGA-G3-A5SJ 
       11.97 

$subtype3
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5262 TCGA-DD-A119 
       46.78        27.52        25.32        69.57         3.39         7.33 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       10.78        56.25        61.45         3.19        23.01        14.40 
TCGA-FV-A495 TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
        0.03        28.27        21.53        22.13        25.64         5.88 
TCGA-G3-A5SK TCGA-G3-A5SM 
        9.93         4.37 

$subtype4
TCGA-BC-A10U TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       27.52        53.29        79.36        75.65         6.67        13.64 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A4NF 
       21.14        19.73        17.59        20.12         0.36        14.07 
TCGA-DD-A4NG TCGA-DD-A4NP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK 
       14.93        93.67        10.85         7.76         0.62         0.43 
TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL 
        0.39        19.53        19.23         7.99 

$subtype5
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        44.42        13.81         0.26        16.37 
TCGA-BC-A5W4 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        9.50         0.10        83.57         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EJ TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE 
       51.25        66.31        29.16        70.06       102.74        21.67 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 
       15.06        39.75         1.97        32.45        19.07         6.35 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
        0.33         1.22        53.79 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.13     0.03     0.36     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  112.96    60.36    69.57    93.67   102.74 
subtype1 subtype2 subtype3 subtype4 subtype5 
   17.31     7.66    21.83    16.26    19.07 
[1] "0.1 - 113.0 (17.3)" "0.1 - 60.4 (7.7)"   "0.0 - 69.6 (21.8)" 
[4] "0.4 - 93.7 (16.3)"  "0.1 - 102.7 (19.1)"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype4" "subtype2" "subtype3" "subtype5" "subtype5" "subtype3"
 [13] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype1" "subtype1" "subtype5" "subtype2" "subtype1"
 [31] "subtype1" "subtype5" "subtype4" "subtype1" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype5" "subtype4" "subtype5" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype1" "subtype1" "subtype5"
 [49] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [55] "subtype5" "subtype4" "subtype4" "subtype5" "subtype1" "subtype2"
 [61] "subtype4" "subtype1" "subtype1" "subtype1" "subtype5" "subtype4"
 [67] "subtype4" "subtype1" "subtype3" "subtype5" "subtype5" "subtype3"
 [73] "subtype1" "subtype3" "subtype4" "subtype2" "subtype2" "subtype1"
 [79] "subtype4" "subtype4" "subtype2" "subtype5" "subtype4" "subtype3"
 [85] "subtype4" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [91] "subtype5" "subtype1" "subtype3" "subtype5" "subtype2" "subtype4"
 [97] "subtype5" "subtype1" "subtype5" "subtype3" "subtype1" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4"
[109] "subtype2" "subtype3" "subtype4" "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype4" "subtype2" "subtype3" "subtype5" "subtype5" "subtype3"
 [13] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype1" "subtype1" "subtype5" "subtype2" "subtype1"
 [31] "subtype1" "subtype5" "subtype4" "subtype1" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype5" "subtype4" "subtype5" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype1" "subtype1" "subtype5"
 [49] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [55] "subtype5" "subtype4" "subtype4" "subtype5" "subtype1" "subtype2"
 [61] "subtype4" "subtype1" "subtype1" "subtype1" "subtype5" "subtype4"
 [67] "subtype4" "subtype1" "subtype3" "subtype5" "subtype5" "subtype3"
 [73] "subtype1" "subtype3" "subtype4" "subtype2" "subtype2" "subtype1"
 [79] "subtype4" "subtype4" "subtype2" "subtype5" "subtype4" "subtype3"
 [85] "subtype4" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [91] "subtype5" "subtype1" "subtype3" "subtype5" "subtype2" "subtype4"
 [97] "subtype5" "subtype1" "subtype5" "subtype3" "subtype1" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4"
[109] "subtype2" "subtype3" "subtype4" "subtype3"
  [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype4" "subtype2" "subtype3" "subtype5" "subtype5" "subtype3"
 [13] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [25] "subtype2" "subtype1" "subtype1" "subtype5" "subtype2" "subtype1"
 [31] "subtype1" "subtype5" "subtype4" "subtype1" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype5" "subtype4" "subtype5" "subtype1"
 [43] "subtype4" "subtype4" "subtype1" "subtype1" "subtype1" "subtype5"
 [49] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
 [55] "subtype5" "subtype4" "subtype4" "subtype5" "subtype1" "subtype2"
 [61] "subtype4" "subtype1" "subtype1" "subtype1" "subtype5" "subtype4"
 [67] "subtype4" "subtype1" "subtype3" "subtype5" "subtype5" "subtype3"
 [73] "subtype1" "subtype3" "subtype4" "subtype2" "subtype2" "subtype1"
 [79] "subtype4" "subtype4" "subtype2" "subtype5" "subtype4" "subtype3"
 [85] "subtype4" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
 [91] "subtype5" "subtype1" "subtype3" "subtype5" "subtype2" "subtype4"
 [97] "subtype5" "subtype1" "subtype5" "subtype3" "subtype1" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype4"
[109] "subtype2" "subtype3" "subtype4" "subtype3"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8        9         1          4          1          2        0
  subtype2       2        3         0          7          1          1        0
  subtype3      10        3         0          2          0          1        1
  subtype4       9        6         0          6          0          0        0
  subtype5      14        4         1          6          0          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         1         0
  subtype4         0         0
  subtype5         0         0
D3V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  8 11  8  2
  subtype2  2  3  8  2
  subtype3 12  3  4  2
  subtype4  9  7  6  0
  subtype5 15  4  7  1
D3V4, multiclass
D3V5, binary
          cls
clus        0  1
  subtype1 22  1
  subtype2 10  0
  subtype3 10  1
  subtype4 13  0
  subtype5 18  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    1
  subtype2   10    0
  subtype3   10    1
  subtype4   13    0
  subtype5   18    1
          vv
clus       M0 M1 MX
  subtype1 25  1  4
  subtype2 11  0  4
  subtype3 12  1  8
  subtype4 17  0  5
  subtype5 23  0  4
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1 20 10
  subtype2  3 12
  subtype3  3 18
  subtype4  1 21
  subtype5 17 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   10
  subtype2    3   12
  subtype3    3   18
  subtype4    1   21
  subtype5   17   10
          vv
clus       R0 R1 R2 RX
  subtype1 24  2  0  4
  subtype2 10  3  0  1
  subtype3 16  2  1  0
  subtype4 19  1  0  0
  subtype5 22  2  0  3
D3V8, multiclass

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 24 17
  subtype2 24 26
  subtype3 13  8
subtype1 subtype2 subtype3 
      41       50       21 
subtype1 subtype2 subtype3 
      17       26        8 
$subtype1
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5262 TCGA-CC-A3MB 
       13.81         0.26        16.37         9.50         3.39         0.10 
TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
       83.57         2.60         0.46        21.76        51.25        66.31 
TCGA-DD-A1EI TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NI 
        6.02        70.06       102.74        73.38        21.67        10.78 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NO TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QR 
       15.06        39.75        61.45         3.19        23.01        19.07 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z 
        6.35         0.03         0.33        53.79        28.27        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SK TCGA-G3-A5SM 
       22.13        25.64         5.88         9.93         4.37 

$subtype2
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-A216 TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       44.42         0.07         0.16         2.86         3.02         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        37.74 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
      112.96         7.33        19.76        12.95        49.15        29.16 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.66         5.59        19.73         7.66        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NN 
      107.11        13.78        30.58        33.14        14.24        29.56 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HT 
       12.26         0.23         0.20        11.74         1.97        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       32.45         0.20         0.13        60.36        51.02        58.49 
TCGA-G3-A25Y TCGA-G3-A5SJ 
       14.86        11.97 

$subtype3
TCGA-BC-A10U TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       27.52        53.29        79.36        75.65         6.67        13.64 
TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NL TCGA-DD-A4NP 
       21.14         0.36        14.07        14.93        56.25        93.67 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A25S 
       10.85         7.76         0.62         0.43         0.39         1.22 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL 
       19.53        19.23         7.99 

subtype1 subtype2 subtype3 
    0.03     0.07     0.36 
subtype1 subtype2 subtype3 
  102.74   112.96    93.67 
subtype1 subtype2 subtype3 
   21.53    14.01    14.07 
[1] "0.0 - 102.7 (21.5)" "0.1 - 113.0 (14.0)" "0.4 - 93.7 (14.1)" 
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
  [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [73] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [97] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype1"
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
  [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [73] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [97] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype1"
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
  [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [61] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
 [67] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [73] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [79] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
 [85] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [91] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [97] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[109] "subtype2" "subtype1" "subtype3" "subtype1"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      22        7         1          7          0          1        0
  subtype2      11       13         1         13          2          4        1
  subtype3      10        5         0          5          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         0
D4V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 24  7  9  3
  subtype2 12 15 19  4
  subtype3 10  6  5  0
D4V4, multiclass
D4V5, binary
          cls
clus        0  1
  subtype1 27  1
  subtype2 33  2
  subtype3 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    1
  subtype2   33    2
  subtype3   13    0
   clus
vv  subtype1 subtype2 subtype3
  0       27       33       13
  1        1        2        0
          vv
clus       M0 M1 MX
  subtype1 32  0 11
  subtype2 40  2  9
  subtype3 16  0  5
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1 18 25
  subtype2 26 25
  subtype3  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   25
  subtype2   26   25
  subtype3    0   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       26        0
  MALE         25       25       21
          vv
clus       R0 R1 R2 RX
  subtype1 35  3  0  3
  subtype2 39  5  1  5
  subtype3 17  2  0  0
D4V8, multiclass

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  7  4
  subtype2  3  7
  subtype3 14 14
  subtype4 12 11
  subtype5 24 14
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       10       28       23       38 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        7       14       11       14 
$subtype1
TCGA-BC-4072 TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 
       48.99        25.32        69.57         0.07         0.16         0.10 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-FV-A23B TCGA-FV-A4ZQ 
       75.65        49.15        29.16        32.45         0.39 

$subtype2
TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A115 
       27.91         1.12         3.39         4.24         3.32        83.57 
TCGA-DD-A1EL TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S 
       13.64         3.19         0.03         1.22 

$subtype3
TCGA-BC-A10Q TCGA-BC-A112 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC 
       37.32         5.03         2.86         3.02         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 
       37.74         7.33        12.95         6.02        55.66        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI 
       30.58        33.14        73.38        21.67        14.24        10.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-ED-A5KG TCGA-ES-A2HT 
       56.25        29.56        61.45        93.67         0.20        14.40 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A25Y 
        0.20        51.02        58.49        14.86 

$subtype4
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-CC-A3MB TCGA-DD-A11D 
       10.13        46.78        27.52        23.34         0.10        51.25 
TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-EP-A2KA 
       66.31         5.59        70.06       102.74        13.78        11.74 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QR TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.62         0.43        19.07        28.27        30.71        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A5SM 
       22.13        25.64         5.88        11.97         4.37 

$subtype5
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       27.52         2.99        44.42        13.81         0.26        16.37 
TCGA-BC-A5W4 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        9.50        79.73        53.29       112.96         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z 
       21.76        79.36        19.76         6.67        21.14        19.73 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NF 
        7.66        17.59        20.12       107.11         0.36        14.07 
TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-ED-A459 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       14.93        12.26         0.23        10.85         7.76         1.97 
TCGA-ES-A2HS TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK 
       23.01         0.33        60.36        53.79        19.53        19.23 
TCGA-G3-A5SK TCGA-G3-A5SL 
        9.93         7.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.03     0.07     0.10     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
   75.65    83.57    93.67   102.74   112.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
  29.160    3.355   18.265   21.530   15.650 
[1] "0.1 - 75.7 (29.2)"  "0.0 - 83.6 (3.4)"   "0.1 - 93.7 (18.3)" 
[4] "0.1 - 102.7 (21.5)" "0.2 - 113.0 (15.7)"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
  [7] "subtype5" "subtype5" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
 [31] "subtype3" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype4" "subtype5" "subtype4" "subtype5"
 [43] "subtype1" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype3"
 [55] "subtype5" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
 [61] "subtype4" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype5" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype5"
 [79] "subtype5" "subtype4" "subtype5" "subtype4" "subtype2" "subtype4"
 [85] "subtype5" "subtype3" "subtype1" "subtype4" "subtype3" "subtype2"
 [91] "subtype5" "subtype5" "subtype1" "subtype2" "subtype3" "subtype5"
 [97] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
[109] "subtype5" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
  [7] "subtype5" "subtype5" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
 [31] "subtype3" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype4" "subtype5" "subtype4" "subtype5"
 [43] "subtype1" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype3"
 [55] "subtype5" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
 [61] "subtype4" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype5" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype5"
 [79] "subtype5" "subtype4" "subtype5" "subtype4" "subtype2" "subtype4"
 [85] "subtype5" "subtype3" "subtype1" "subtype4" "subtype3" "subtype2"
 [91] "subtype5" "subtype5" "subtype1" "subtype2" "subtype3" "subtype5"
 [97] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
[109] "subtype5" "subtype4"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype4"
  [7] "subtype5" "subtype5" "subtype1" "subtype4" "subtype2" "subtype1"
 [13] "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
 [31] "subtype3" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [37] "subtype5" "subtype5" "subtype4" "subtype5" "subtype4" "subtype5"
 [43] "subtype1" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype3"
 [55] "subtype5" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
 [61] "subtype4" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype5" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype5"
 [79] "subtype5" "subtype4" "subtype5" "subtype4" "subtype2" "subtype4"
 [85] "subtype5" "subtype3" "subtype1" "subtype4" "subtype3" "subtype2"
 [91] "subtype5" "subtype5" "subtype1" "subtype2" "subtype3" "subtype5"
 [97] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype4" "subtype4" "subtype5" "subtype5" "subtype4" "subtype5"
[109] "subtype5" "subtype4"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       2        2         1          4          0          2        0
  subtype2       3        2         0          4          0          1        0
  subtype3      11        6         0          3          1          2        1
  subtype4      11        2         1          4          2          0        0
  subtype5      15       12         0         10          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         0
  subtype3         0         1
  subtype4         1         0
  subtype5         0         0
D5V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  4  2  5  1
  subtype2  3  2  4  1
  subtype3 11  8  6  2
  subtype4 12  2  9  2
  subtype5 15 13 10  1
D5V4, multiclass
D5V5, binary
          cls
clus        0  1
  subtype1  9  1
  subtype2  8  0
  subtype3 19  1
  subtype4 14  1
  subtype5 23  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2    8    0
  subtype3   19    1
  subtype4   14    1
  subtype5   23    0
          vv
clus       M0 M1 MX
  subtype1 10  0  2
  subtype2  7  0  3
  subtype3 23  2  3
  subtype4 16  0  9
  subtype5 33  0  6
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1  7  5
  subtype2  2  8
  subtype3 14 14
  subtype4  8 17
  subtype5 12 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2    2    8
  subtype3   14   14
  subtype4    8   17
  subtype5   12   27
          vv
clus       R0 R1 R2 RX
  subtype1  9  1  0  2
  subtype2  4  2  0  1
  subtype3 24  1  1  2
  subtype4 21  2  0  1
  subtype5 31  4  0  3
D5V8, multiclass

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  6
  subtype2 35 21
  subtype3 22 23
subtype1 subtype2 subtype3 
       9       56       45 
subtype1 subtype2 subtype3 
       6       21       23 
$subtype1
TCGA-BC-4073 TCGA-BC-A10Z TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A1EL 
       27.91         1.12         3.39         3.32        83.57        13.64 
TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S 
        3.19         0.03         1.22 

$subtype2
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 
       10.13        27.52        27.52        23.34        44.42        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A3MB 
        0.26        16.37         9.50         0.16         4.24         0.10 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       79.73        53.29       112.96         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Y 
       51.25        79.36        66.31         6.67        21.14         5.59 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       19.73         7.66        70.06       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-EP-A12J 
        0.36        14.07        14.93        93.67        12.26        10.85 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QR 
        7.76        11.74         1.97         0.62         0.43        19.07 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.33        60.36        53.79        28.27        30.71        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       22.13         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

$subtype3
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 
       48.99        37.32        46.78         2.99        25.32        69.57 
TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MA 
        5.03         0.07         2.86         3.02         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
        0.13        37.74         7.33        19.76        75.65        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A3 
       49.15         6.02        29.16        55.66        25.81        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH 
       20.12        30.58        33.14        73.38        21.67        14.24 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-ED-A459 TCGA-ED-A5KG 
       10.78        56.25        29.56        61.45         0.23         0.20 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
       23.01        14.40        32.45         0.20         0.39        51.02 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       58.49        14.86        25.64 

subtype1 subtype2 subtype3 
    0.03     0.10     0.07 
subtype1 subtype2 subtype3 
   83.57   112.96    75.65 
subtype1 subtype2 subtype3 
    3.32    14.50    21.67 
[1] "0.0 - 83.6 (3.3)"   "0.1 - 113.0 (14.5)" "0.1 - 75.7 (21.7)" 
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2"
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2"
  [1] "subtype3" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       3        2         0          3          0          1        0
  subtype2      24       13         1         13          2          1        0
  subtype3      15        9         1          9          1          3        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
D6V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  3  2  3  1
  subtype2 25 14 17  3
  subtype3 17 11 14  3
D6V4, multiclass
D6V5, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2 35  1
  subtype3 31  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   35    1
  subtype3   31    2
   clus
vv  subtype1 subtype2 subtype3
  0        7       35       31
  1        0        1        2
          vv
clus       M0 M1 MX
  subtype1  6  0  3
  subtype2 47  0 12
  subtype3 36  2  8
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  2  7
  subtype2 20 39
  subtype3 21 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2   20   39
  subtype3   21   25
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2       20       21
  MALE          7       39       25
          vv
clus       R0 R1 R2 RX
  subtype1  4  2  0  0
  subtype2 47  5  0  5
  subtype3 38  3  1  4
D6V8, multiclass

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 15 10
  subtype2 25 26
  subtype3 20 14
subtype1 subtype2 subtype3 
      25       51       34 
subtype1 subtype2 subtype3 
      10       26       14 
$subtype1
TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-CC-5258 TCGA-CC-5259 
       48.99        27.52        25.32        69.57         0.07         0.16 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A1EB 
        3.39         0.10         0.10        83.57         7.33        66.31 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A3A5 TCGA-EP-A3JL 
       75.65        49.15         6.02        29.16       102.74         3.19 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25V TCGA-G3-A25W 
       14.40        32.45         0.03         0.39        28.27        30.71 
TCGA-G3-A5SK 
        9.93 

$subtype2
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        46.78        27.52         2.99        23.34         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5263 
       44.42        13.81         0.26        16.37         9.50         4.24 
TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        3.32        79.73        53.29       112.96         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V 
       21.76        51.25        79.36         6.67        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.59        19.73         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-EP-A12J 
      107.11        13.78         0.36        14.07        14.93        10.85 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QR 
        7.76         1.97         0.62         0.43        23.01        19.07 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
        0.33         1.22        53.79        21.53        22.13         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL 
       19.53        19.23         7.99 

$subtype3
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MA 
       37.32        10.13         5.03         2.86         3.02         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39X TCGA-DD-A3A0 
        0.13        37.74        19.76        12.95        55.66        25.81 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI 
       30.58        33.14        73.38        21.67        14.24        10.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A459 
       56.25        29.56        61.45        93.67        12.26         0.23 
TCGA-ED-A5KG TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
        0.20        11.74         0.20        60.36        51.02        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SJ TCGA-G3-A5SM 
       14.86        25.64        11.97         4.37 

subtype1 subtype2 subtype3 
    0.03     0.26     0.07 
subtype1 subtype2 subtype3 
  102.74   112.96    93.67 
subtype1 subtype2 subtype3 
   25.32    14.93    17.31 
[1] "0.0 - 102.7 (25.3)" "0.3 - 113.0 (14.9)" "0.1 - 93.7 (17.3)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype2" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype2" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [25] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [43] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [91] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [97] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype2" "subtype3"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8        3         2          6          1          3        1
  subtype2      23       12         0         13          1          0        0
  subtype3      11        9         0          6          1          2        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         0
  subtype3         1         1
D7V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 10  3 10  3
  subtype2 23 13 15  2
  subtype3 12 11  9  2
D7V4, multiclass
D7V5, binary
          cls
clus        0  1
  subtype1 18  1
  subtype2 34  0
  subtype3 21  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2   34    0
  subtype3   21    2
   clus
vv  subtype1 subtype2 subtype3
  0       18       34       21
  1        1        0        2
          vv
clus       M0 M1 MX
  subtype1 20  1  5
  subtype2 40  0 13
  subtype3 29  1  5
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1 11 15
  subtype2 15 38
  subtype3 17 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   15
  subtype2   15   38
  subtype3   17   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11       15       17
  MALE         15       38       18
          vv
clus       R0 R1 R2 RX
  subtype1 19  2  1  2
  subtype2 39  6  0  5
  subtype3 31  2  0  2
D7V8, multiclass

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 22 16
  subtype2  3  7
  subtype3 35 27
subtype1 subtype2 subtype3 
      38       10       62 
subtype1 subtype2 subtype3 
      16        7       27 
$subtype1
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-CC-5258 
       37.32         2.99        25.32        69.57         5.03         0.07 
TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        2.86         0.10         0.07         0.10         0.13        37.74 
TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        7.33        19.76        75.65        49.15         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A3A3 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NE 
       55.66        17.59        30.58        33.14        73.38        21.67 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-ED-A459 
       14.24        10.78        56.25        29.56        61.45         0.23 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       14.40        32.45         0.20         0.39        51.02        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH 
       14.86        25.64 

$subtype2
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-A1EL TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S 
       13.64         3.19         0.03         1.22 

$subtype3
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-CC-5259 TCGA-CC-5261 
       13.81         0.26        16.37         9.50         0.16         3.02 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
        4.24        79.73        53.29       112.96         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF 
       21.76        51.25        79.36        66.31         6.67        12.95 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.59        19.73        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NF 
       20.12       102.74       107.11        13.78         0.36        14.07 
TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-ED-A5KG TCGA-EP-A12J TCGA-EP-A26S 
       14.93        93.67        12.26         0.20        10.85         7.76 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QR 
       11.74         1.97         0.62         0.43        23.01        19.07 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.33        60.36        53.79        28.27        30.71        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       22.13         5.88        19.53        19.23        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM 
        7.99         4.37 

subtype1 subtype2 subtype3 
    0.07     0.03     0.16 
subtype1 subtype2 subtype3 
   75.65    83.57   112.96 
subtype1 subtype2 subtype3 
  20.715    3.355   15.650 
[1] "0.1 - 75.7 (20.7)"  "0.0 - 83.6 (3.4)"   "0.2 - 113.0 (15.7)"
  [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3"
  [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3"
  [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
 [13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
 [61] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [67] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [73] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      12        7         1          8          1          3        1
  subtype2       3        2         0          4          0          1        0
  subtype3      27       15         1         13          2          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         1         0
D8V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1 14  9 12  3
  subtype2  3  2  4  1
  subtype3 28 16 18  3
D8V4, multiclass
D8V5, binary
          cls
clus        0  1
  subtype1 27  2
  subtype2  8  0
  subtype3 38  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    2
  subtype2    8    0
  subtype3   38    1
   clus
vv  subtype1 subtype2 subtype3
  0       27        8       38
  1        2        0        1
          vv
clus       M0 M1 MX
  subtype1 31  2  6
  subtype2  7  0  3
  subtype3 51  0 14
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1 18 21
  subtype2  3  7
  subtype3 22 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   21
  subtype2    3    7
  subtype3   22   43
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18        3       22
  MALE         21        7       43
          vv
clus       R0 R1 R2 RX
  subtype1 33  2  1  3
  subtype2  4  3  0  0
  subtype3 52  5  0  6
D8V8, multiclass
> q(save="no")
