
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/READ-TP/6159710/READ-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/6154781/READ-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=READ-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=READ-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/READ-TP/6154781/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/6159710/READ-TP.mergedcluster.txt"

nPatients in clinical file=168, in cluster file=166, common to both=166
[1]  12 166
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
25 22 22 
 1  2  3 
25 22 22 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
24 29 16 
 1  2  3 
24 29 16 
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5  6 
10 34 42 30 24 22 
 1  2  3  4  5  6 
10 34 42 30 24 22 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
25 39 31 
 1  2  3 
25 39 31 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
33 43 54 
 1  2  3 
33 43 54 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 6 19 33 26 46 
 1  2  3  4  5 
 6 19 33 26 46 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
59 31 66 
 1  2  3 
59 31 66 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
67  7 51 31 
 1  2  3  4 
67  7 51 31 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
18 42 17 10 56 
 1  2  3  4  5 
18 42 17 10 56 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
20 64 59 
 1  2  3 
20 64 59 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
12 22 23 18 
 1  2  3  4 
12 22 23 18 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 9 20 14 10 22 
 1  2  3  4  5 
 9 20 14 10 22 
[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] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE"                         
[19] "PSA_VALUE"                             
[20] "DAYS_TO_PSA"                           
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 166 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         734          546          524          323          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-4110 TCGA-AF-5654 
         387          761          316          390          441          257 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
         467          355          316           NA          365           NA 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
          NA           31           31           61           NA           31 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
          31           NA           NA           NA           NA           NA 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 
          30           NA           NA           NA           30           NA 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
          NA           NA           NA           NA          242           29 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
          NA           31           NA           30           30           NA 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3891 
          NA           31           NA           28           NA           30 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
          31           30           30           31           NA           NA 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
          NA           NA           31           31           NA           31 
TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
          31           NA           NA           30          637          423 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
         183          789          700          518          484          396 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
          31           31          365          365         2130         1946 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
         334           NA         1519           NA           NA         1884 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
        1246         1156         2192           15           44            6 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
          21           22          140           55          310          183 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
         183           NA          211          285          143          425 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        1825          243          334          335          457          395 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
         365          426          457         1095          212          914 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
         394          396          306          161         3845         1257 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        1741         3932          734         1566          991           15 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
          73          625          607          636          517          556 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
         482          538          497          496          498          262 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         350          328          414          531          364          257 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
          NA          103           26           66           12           31 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
          20           21           16           33           23           14 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=96,	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=11,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 166 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  30 112  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  30 112  14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  30 112  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  30 112  14 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
84 45 34 
[1] "table(vv)"
vv
N0 N1 N2 
84 45 34 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
84 45 34 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
84 45 34 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 20  1
  subtype2 10  0
  subtype3 10  3
subtype1 subtype2 subtype3 
      21       10       13 
subtype1 subtype2 subtype3 
       1        0        3 
$subtype1
TCGA-AF-2689 TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3726 
       17.95        13.55         2.01         1.02         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        0.95         0.92         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.94        23.01        17.03        13.02         1.02        12.00 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X 
       49.94        38.93        40.96 

$subtype2
TCGA-AF-2691 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 
       10.62        12.72        12.00         1.02         1.02         1.02 
TCGA-AG-3605 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 
        0.99         0.99         1.02         1.02 

$subtype3
TCGA-AF-3913 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       10.39         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A026 
        1.02        15.91         1.02        12.00        51.98         1.94 
TCGA-AG-A032 
       38.01 

subtype1 subtype2 subtype3 
    0.92     0.99     0.99 
subtype1 subtype2 subtype3 
   49.94    12.72    51.98 
subtype1 subtype2 subtype3 
   13.02     1.02     1.02 
[1] "0.9 - 49.9 (13.0)" "1.0 - 12.7 (1.0)"  "1.0 - 52.0 (1.0)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[37] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[43] "subtype1" "subtype3"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       8        1         7         2          3          0        4
  subtype2       7        1         8         0          2          2        2
  subtype3       3        1         5         0          5          2        5
D1V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  3  6 16  0
  subtype2  2  5 15  0
  subtype3  0  4 14  4
D1V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 16  5  4
  subtype2 16  4  2
  subtype3 10  6  6
D1V5, multiclass
          vv
clus       M0 M1
  subtype1 21  4
  subtype2 20  2
  subtype3 16  6
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       21       20       16
  M1        4        2        6
D1V7, binary
          cls
clus        0  1
  subtype1 12 13
  subtype2  9 13
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   13
  subtype2    9   13
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12        9       10
  MALE         13       13       12
D1V8, binary
          cls
clus        0  1
  subtype1 19  3
  subtype2 18  3
  subtype3 21  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    3
  subtype2   18    3
  subtype3   21    1
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                19       18       21
  RECTAL MUCINOUS ADENOCARCINOMA        3        3        1
D1V9, binary
          cls
clus        0  1
  subtype1  0 25
  subtype2  1 21
  subtype3  0 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   25
  subtype2    1   21
  subtype3    0   22
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        0
  YES       25       21       22
          vv
clus       R0 R1 R2
  subtype1 22  0  3
  subtype2 19  0  2
  subtype3 16  1  5
D1V10, multiclass
D1V11, continuous

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 19  2
  subtype2 13  2
  subtype3  8  0
subtype1 subtype2 subtype3 
      21       15        8 
subtype1 subtype2 subtype3 
       2        2        0 
$subtype1
TCGA-AF-2689 TCGA-AF-2692 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
       17.95        13.55         1.02         0.99         7.96         0.95 
TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        0.92         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 
       23.01        15.91        13.02         1.02        12.00        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X 
       49.94        38.93        40.96 

$subtype2
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3893 
       12.72        10.39         1.02         0.99         1.02         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A01J 
        1.02         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 
       12.00         1.94        38.01 

$subtype3
TCGA-AF-2691 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3605 
       10.62        12.00         1.02         2.01         1.02         0.99 
TCGA-AG-3892 TCGA-AG-A011 
        1.02        17.03 

subtype1 subtype2 subtype3 
    0.92     0.99     0.99 
subtype1 subtype2 subtype3 
   51.98    38.01    17.03 
subtype1 subtype2 subtype3 
  13.550    1.020    1.515 
[1] "0.9 - 52.0 (13.6)" "1.0 - 38.0 (1.0)"  "1.0 - 17.0 (1.5)" 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[43] "subtype1" "subtype2"
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[43] "subtype1" "subtype2"
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[43] "subtype1" "subtype2"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC STAGE IV
  subtype1       9        1         6         2          2          0        4
  subtype2       5        1         8         0          7          2        5
  subtype3       4        1         6         0          1          2        2
D2V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  3  7 13  1
  subtype2  0  6 20  3
  subtype3  2  2 12  0
D2V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 16  4  4
  subtype2 15  9  5
  subtype3 11  2  3
D2V5, multiclass
          vv
clus       M0 M1
  subtype1 20  4
  subtype2 23  6
  subtype3 14  2
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       20       23       14
  M1        4        6        2
D2V7, binary
          cls
clus        0  1
  subtype1 12 12
  subtype2 13 16
  subtype3  6 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   12
  subtype2   13   16
  subtype3    6   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       13        6
  MALE         12       16       10
D2V8, binary
          cls
clus        0  1
  subtype1 19  2
  subtype2 25  3
  subtype3 14  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    2
  subtype2   25    3
  subtype3   14    2
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                19       25       14
  RECTAL MUCINOUS ADENOCARCINOMA        2        3        2
D2V9, binary
          cls
clus        0  1
  subtype1  0 24
  subtype2  1 28
  subtype3  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   24
  subtype2    1   28
  subtype3    0   16
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        0
  YES       24       28       16
          vv
clus       R0 R1 R2
  subtype1 21  0  3
  subtype2 22  1  5
  subtype3 14  0  2
D2V10, multiclass
D2V11, continuous

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 10  0
  subtype2 19  4
  subtype3 36  0
  subtype4 19  3
  subtype5 18  2
  subtype6 15  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      10       23       36       22       20       19 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       0        4        0        3        2        4 
$subtype1
TCGA-AF-2687 TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-6155 TCGA-DY-A1DE TCGA-EI-6885 
       24.13         9.37        13.97        14.01       129.27        13.61 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        3.39         0.39         0.66         0.69 

$subtype2
TCGA-AF-2689 TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3742 TCGA-AG-4001 TCGA-AG-4007 
       17.95        17.23         1.02         0.99         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A026 TCGA-DC-4745 TCGA-DC-4749 
        1.02         1.02        12.00         1.94        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DG TCGA-EI-6511 
       12.99        12.00        36.00        10.06        51.48        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-F5-6811 TCGA-G5-6572 
       17.69        16.34        16.31         1.02        47.08 

$subtype3
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       10.62        12.72         8.45        12.00         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A011 
        0.99         0.99         1.02         0.99        20.94        17.03 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       10.98        49.94         0.49         1.45         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6681 
        6.02         6.02         6.94         4.70        15.02        12.95 
TCGA-DT-5265 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6882 
        5.29        20.55        19.96        20.91        18.28         8.61 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
       10.78        17.46         8.45         0.53         1.08        55.76 

$subtype4
TCGA-AF-2692 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       13.55        10.39         1.02         7.96         0.95         1.02 
TCGA-AG-3883 TCGA-AG-A008 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02G TCGA-AG-A02N 
        1.02        13.91        70.03        63.98        38.93        61.94 
TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1H8 
       40.96         0.69        10.19        30.05        13.02        32.58 
TCGA-EF-5831 TCGA-EI-7002 TCGA-G5-6233 TCGA-G5-6641 
        2.40        11.97        18.25        26.43 

$subtype5
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3893 
       19.10        25.02        10.39        14.50        15.35         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02         0.99         6.02        25.94        23.01 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A032 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6881 
       13.02        12.00        38.01        15.02        24.13        16.37 
TCGA-F5-6571 TCGA-F5-6702 
        0.85         2.17 

$subtype6
TCGA-AF-6655 TCGA-AG-3586 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-A014 TCGA-AG-A01J 
       11.67         1.02         0.99         0.92        15.91         1.02 
TCGA-AG-A023 TCGA-AH-6644 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6158 TCGA-DY-A0XA 
       51.98         0.72        60.00         7.99         6.97       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6883 TCGA-F5-6863 
       41.33        57.24         0.49        17.00        11.51         0.76 
TCGA-F5-6864 
        0.46 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.39     0.99     0.49     0.69     0.85     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  129.27    51.48    55.76    70.03    38.01   126.41 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  11.490   12.000    8.450   13.285   13.760    7.990 
[1] "0.4 - 129.3 (11.5)" "1.0 - 51.5 (12.0)"  "0.5 - 55.8 (8.4)"  
[4] "0.7 - 70.0 (13.3)"  "0.8 - 38.0 (13.8)"  "0.5 - 126.4 (8.0)" 
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype4" "subtype5"
  [7] "subtype3" "subtype5" "subtype5" "subtype5" "subtype3" "subtype5"
 [13] "subtype6" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype6" "subtype4" "subtype3" "subtype6" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype3" "subtype4" "subtype6" "subtype3"
 [31] "subtype5" "subtype3" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype5"
 [43] "subtype5" "subtype3" "subtype6" "subtype5" "subtype2" "subtype6"
 [49] "subtype5" "subtype2" "subtype4" "subtype4" "subtype3" "subtype6"
 [55] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [61] "subtype3" "subtype3" "subtype4" "subtype6" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype6" "subtype6" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype2" "subtype1" "subtype5" "subtype2" "subtype6"
 [85] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype6"
 [91] "subtype6" "subtype6" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype6" "subtype4" "subtype3" "subtype3" "subtype3" "subtype6"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype5"
[109] "subtype3" "subtype6" "subtype3" "subtype1" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype6" "subtype6"
[127] "subtype4" "subtype3" "subtype2" "subtype4"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype4" "subtype5"
  [7] "subtype3" "subtype5" "subtype5" "subtype5" "subtype3" "subtype5"
 [13] "subtype6" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype6" "subtype4" "subtype3" "subtype6" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype3" "subtype4" "subtype6" "subtype3"
 [31] "subtype5" "subtype3" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype5"
 [43] "subtype5" "subtype3" "subtype6" "subtype5" "subtype2" "subtype6"
 [49] "subtype5" "subtype2" "subtype4" "subtype4" "subtype3" "subtype6"
 [55] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [61] "subtype3" "subtype3" "subtype4" "subtype6" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype6" "subtype6" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype2" "subtype1" "subtype5" "subtype2" "subtype6"
 [85] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype6"
 [91] "subtype6" "subtype6" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype6" "subtype4" "subtype3" "subtype3" "subtype3" "subtype6"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype5"
[109] "subtype3" "subtype6" "subtype3" "subtype1" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype6" "subtype6"
[127] "subtype4" "subtype3" "subtype2" "subtype4"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype4" "subtype5"
  [7] "subtype3" "subtype5" "subtype5" "subtype5" "subtype3" "subtype5"
 [13] "subtype6" "subtype4" "subtype3" "subtype3" "subtype2" "subtype3"
 [19] "subtype6" "subtype4" "subtype3" "subtype6" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype3" "subtype4" "subtype6" "subtype3"
 [31] "subtype5" "subtype3" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype3" "subtype4" "subtype5" "subtype5"
 [43] "subtype5" "subtype3" "subtype6" "subtype5" "subtype2" "subtype6"
 [49] "subtype5" "subtype2" "subtype4" "subtype4" "subtype3" "subtype6"
 [55] "subtype3" "subtype2" "subtype4" "subtype4" "subtype4" "subtype5"
 [61] "subtype3" "subtype3" "subtype4" "subtype6" "subtype3" "subtype3"
 [67] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [73] "subtype1" "subtype6" "subtype6" "subtype2" "subtype2" "subtype3"
 [79] "subtype2" "subtype2" "subtype1" "subtype5" "subtype2" "subtype6"
 [85] "subtype4" "subtype3" "subtype4" "subtype2" "subtype3" "subtype6"
 [91] "subtype6" "subtype6" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype6" "subtype4" "subtype3" "subtype3" "subtype3" "subtype6"
[103] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype5"
[109] "subtype3" "subtype6" "subtype3" "subtype1" "subtype3" "subtype4"
[115] "subtype3" "subtype1" "subtype5" "subtype5" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype6" "subtype6"
[127] "subtype4" "subtype3" "subtype2" "subtype4"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0         4         0         0         0          2
  subtype2       4        2         9         0         0         0          0
  subtype3      13        2         8         1         0         1          3
  subtype4       6        3         7         0         1         2          2
  subtype5       3        1         3         0         0         1          1
  subtype6       3        0         7         1         1         1          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          0          2        1         0
  subtype2          9          1        6         2
  subtype3          4          2        2         4
  subtype4          1          3        5         0
  subtype5          7          3        1         3
  subtype6          2          3        2         0
D3V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  1  7  1
  subtype2  1  4 24  4
  subtype3  5 10 24  3
  subtype4  1  8 20  1
  subtype5  1  2 19  2
  subtype6  0  4 15  3
D3V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  5  3  2
  subtype2 16 11  6
  subtype3 27 10  5
  subtype4 16  7  7
  subtype5  7 10  7
  subtype6 12  4  5
D3V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1  9  1   0  0
  subtype2 25  8   0  0
  subtype3 34  4   1  3
  subtype4 22  4   0  3
  subtype5 16  3   1  4
  subtype6 17  2   0  3
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1  5  5
  subtype2 18 16
  subtype3 17 25
  subtype4 11 19
  subtype5 10 14
  subtype6 13  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    5
  subtype2   18   16
  subtype3   17   25
  subtype4   11   19
  subtype5   10   14
  subtype6   13    9
D3V8, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 34  0
  subtype3 33  8
  subtype4 24  4
  subtype5 22  0
  subtype6 20  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   34    0
  subtype3   33    8
  subtype4   24    4
  subtype5   22    0
  subtype6   20    1
D3V9, binary
          cls
clus        0  1
  subtype1  1  9
  subtype2  0 34
  subtype3  1 41
  subtype4  2 28
  subtype5  2 22
  subtype6  0 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    0   34
  subtype3    1   41
  subtype4    2   28
  subtype5    2   22
  subtype6    0   22
          vv
clus       R0 R1 R2 RX
  subtype1  7  0  0  0
  subtype2 24  1  6  0
  subtype3 33  1  1  1
  subtype4 23  0  3  0
  subtype5 20  0  0  0
  subtype6 14  0  2  2
D3V10, multiclass
D3V11, continuous

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 23  2
  subtype2 32  4
  subtype3 23  4
subtype1 subtype2 subtype3 
      25       36       27 
subtype1 subtype2 subtype3 
       2        4        4 
$subtype1
TCGA-AF-2687 TCGA-AF-3911 TCGA-AG-4022 TCGA-AG-A01Y TCGA-AH-6549 TCGA-AH-6897 
       24.13        25.02         0.99        63.98         0.20         4.60 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        6.02         4.70        12.99        12.00        15.02        36.00 
TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6513 
        6.97       126.41        57.24       129.27         0.49        16.34 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6864 
       13.61        11.97         3.39         2.17         0.39         0.46 
TCGA-G5-6641 
       26.43 

$subtype2
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       17.23        19.10        14.50        15.35        11.67        10.39 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 
        0.49         1.45         1.81        10.19         6.94         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6160 
       13.97        60.00        10.98        11.01        14.01        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.95        13.02        41.33        32.58        20.55        19.96 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6571 
       17.00        15.85        16.37        10.78        17.46         0.85 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.69         1.08         0.76        55.76        47.08 

$subtype3
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N 
        1.02         0.99        70.03        10.98         1.94        61.94 
TCGA-AG-A036 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5337 
       72.07         0.69         0.72         6.02         7.99        15.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6508 
       10.06         5.29        24.13        51.48         2.40        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-7004 
       18.28        17.69        16.31         8.61        11.51         8.45 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        1.02         0.53        18.25 

subtype1 subtype2 subtype3 
    0.20     0.49     0.53 
subtype1 subtype2 subtype3 
  129.27    60.00    72.07 
subtype1 subtype2 subtype3 
  12.000   13.495   10.060 
[1] "0.2 - 129.3 (12.0)" "0.5 - 60.0 (13.5)"  "0.5 - 72.1 (10.1)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[85] "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[85] "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[61] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[73] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[85] "subtype3" "subtype2" "subtype2" "subtype1"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       4        2         4         1         0         0          1
  subtype2       5        0         6         1         0         1          8
  subtype3       2        4         8         0         2         3          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          3        3         3
  subtype2          7          5        1         2
  subtype3          3          2        2         4
D4V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  4 17  3
  subtype2  1  7 24  6
  subtype3  2  2 25  2
D4V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 11  7  6
  subtype2 14 16  8
  subtype3 16  7  7
D4V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 16  5   1  3
  subtype2 27  1   1  8
  subtype3 24  4   0  3
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1 11 14
  subtype2 16 23
  subtype3 15 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   14
  subtype2   16   23
  subtype3   15   16
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11       16       15
  MALE         14       23       16
D4V8, binary
          cls
clus        0  1
  subtype1 24  1
  subtype2 36  1
  subtype3 27  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2   36    1
  subtype3   27    4
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                24       36       27
  RECTAL MUCINOUS ADENOCARCINOMA        1        1        4
D4V9, binary
          cls
clus        0  1
  subtype1  2 23
  subtype2  3 36
  subtype3  0 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   23
  subtype2    3   36
  subtype3    0   31
     clus
vv    subtype1 subtype2 subtype3
  NO         2        3        0
  YES       23       36       31
          vv
clus       R0 R1 R2 RX
  subtype1 18  0  0  1
  subtype2 25  1  0  1
  subtype3 21  1  2  2
D4V10, multiclass
D4V11, continuous

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 21  2
  subtype2 33  4
  subtype3 38  7
subtype1 subtype2 subtype3 
      23       37       45 
subtype1 subtype2 subtype3 
       2        4        7 
$subtype1
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3599 
       17.95        17.23        12.72         1.02         1.02         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-DC-5337 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-F5-6702 
       15.02        15.02        12.95        10.06         5.29         2.17 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        1.02         0.66         0.69         0.76        47.08 

$subtype2
TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3891 TCGA-AG-3893 TCGA-AG-4022 
       10.39        12.82        11.67         0.99         0.99         0.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       25.94        15.91         1.02        12.00        70.03        63.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.94        40.96        72.07         1.45         0.69         0.72 
TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       10.19         7.99        11.01         6.97        30.05        13.02 
TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       41.33        20.55        19.96        15.85        16.34        16.37 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
       17.46         3.39         0.85         1.08         0.46        18.25 
TCGA-G5-6235 
       55.76 

$subtype3
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.45        15.35        10.39         2.01         1.02         1.02 
TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        0.99         0.95         1.02        20.94        13.91         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 
       23.01        17.03        13.02         1.02        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-4745 
        1.94        38.93         0.49         0.20         4.60        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       12.99        14.01        36.00       126.41        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
       24.13        51.48        32.58         0.49         2.40        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 
       17.00        18.28        17.69        16.31         8.61        10.78 
TCGA-EI-6885 TCGA-F5-6810 TCGA-G5-6641 
       13.61         0.39        26.43 

subtype1 subtype2 subtype3 
    0.66     0.46     0.20 
subtype1 subtype2 subtype3 
   47.08    72.07   129.27 
subtype1 subtype2 subtype3 
    1.02    12.82    13.02 
[1] "0.7 - 47.1 (1.0)"   "0.5 - 72.1 (12.8)"  "0.2 - 129.3 (13.0)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
  [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
 [31] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [49] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
 [55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [85] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [91] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
 [97] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[103] "subtype2" "subtype1" "subtype3"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       5        2         7         0         0         0          0
  subtype2       7        4        11         0         1         2          4
  subtype3       9        1        13         1         0         4          4
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          6        5         3
  subtype2          7          2        2         0
  subtype3          8          2        8         2
D5V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  2  3 21  6
  subtype2  0  9 34  0
  subtype3  3 11 36  4
D5V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 14  7 11
  subtype2 25 11  6
  subtype3 25 19  9
D5V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 24  6   2  0
  subtype2 34  3   0  5
  subtype3 40  9   0  5
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1 14 19
  subtype2 16 27
  subtype3 30 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   19
  subtype2   16   27
  subtype3   30   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       16       30
  MALE         19       27       24
D5V8, binary
          cls
clus        0  1
  subtype1 28  3
  subtype2 42  1
  subtype3 47  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    3
  subtype2   42    1
  subtype3   47    6
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                28       42       47
  RECTAL MUCINOUS ADENOCARCINOMA        3        1        6
D5V9, binary
          cls
clus        0  1
  subtype1  1 32
  subtype2  2 41
  subtype3  2 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    2   41
  subtype3    2   52
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        2
  YES       32       41       52
          vv
clus       R0 R1 R2 RX
  subtype1 24  0  5  1
  subtype2 36  1  1  1
  subtype3 37  1  6  1
D5V10, multiclass
D5V11, continuous

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  1
  subtype2 16  1
  subtype3 25  3
  subtype4 12  1
  subtype5 36  7
subtype1 subtype2 subtype3 subtype4 subtype5 
       4       17       28       13       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        1        3        1        7 
$subtype1
TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-F5-6864 
       24.13        20.91        17.00         0.46 

$subtype2
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-A036 
       17.23        12.72        12.82        11.67         1.02        72.07 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6917 
       15.02        12.95        10.06         5.29        19.96        17.46 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
        0.85         2.17         1.08         0.76        55.76 

$subtype3
TCGA-AG-3891 TCGA-AG-3893 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A011 
        0.99         0.99         0.99        20.94        25.94        17.03 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6547 
       15.91        12.00        70.03        63.98        40.96         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        0.69         0.72        10.19         7.99        11.01        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6513 
        6.97        30.05        41.33        20.55        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-F5-6465 TCGA-G5-6233 
       16.37         8.61         3.39        18.25 

$subtype4
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3727 
       17.95        10.39         1.02         0.99         0.99         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4008 
        1.02 

$subtype5
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.45        15.35        10.39         2.01         1.02         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       13.91         6.02        23.01        13.02         1.02         1.02 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 
       10.98        51.98         1.94        38.93        61.94         0.49 
TCGA-AH-6549 TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        0.20         4.60        10.98        12.99        14.01        36.00 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       13.02       126.41        57.24       129.27        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6884 
        0.49         2.40        18.28        17.69        16.31        10.78 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
       13.61         0.39         1.02         0.66         0.69        47.08 
TCGA-G5-6641 
       26.43 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.76     0.69     0.95     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
   24.13    72.07    70.03    17.95   129.27 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.955   12.720   15.435    1.020   12.990 
[1] "0.5 - 24.1 (19.0)"  "0.8 - 72.1 (12.7)"  "0.7 - 70.0 (15.4)" 
[4] "0.9 - 17.9 (1.0)"   "0.2 - 129.3 (13.0)"
  [1] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
  [7] "subtype5" "subtype2" "subtype5" "subtype2" "subtype4" "subtype5"
 [13] "subtype5" "subtype5" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [37] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype5" "subtype3" "subtype2" "subtype5"
 [49] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [61] "subtype2" "subtype5" "subtype3" "subtype3" "subtype2" "subtype5"
 [67] "subtype2" "subtype2" "subtype5" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype5" "subtype3" "subtype5"
 [85] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [91] "subtype2" "subtype3" "subtype2" "subtype2" "subtype5" "subtype5"
 [97] "subtype5" "subtype5" "subtype2" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype5" "subtype5"
  [1] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
  [7] "subtype5" "subtype2" "subtype5" "subtype2" "subtype4" "subtype5"
 [13] "subtype5" "subtype5" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [37] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype5" "subtype3" "subtype2" "subtype5"
 [49] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [61] "subtype2" "subtype5" "subtype3" "subtype3" "subtype2" "subtype5"
 [67] "subtype2" "subtype2" "subtype5" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype5" "subtype3" "subtype5"
 [85] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [91] "subtype2" "subtype3" "subtype2" "subtype2" "subtype5" "subtype5"
 [97] "subtype5" "subtype5" "subtype2" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype5" "subtype5"
  [1] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype5"
  [7] "subtype5" "subtype2" "subtype5" "subtype2" "subtype4" "subtype5"
 [13] "subtype5" "subtype5" "subtype4" "subtype4" "subtype4" "subtype4"
 [19] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [37] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype5" "subtype3" "subtype2" "subtype5"
 [49] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [61] "subtype2" "subtype5" "subtype3" "subtype3" "subtype2" "subtype5"
 [67] "subtype2" "subtype2" "subtype5" "subtype3" "subtype5" "subtype5"
 [73] "subtype1" "subtype5" "subtype5" "subtype5" "subtype5" "subtype3"
 [79] "subtype2" "subtype1" "subtype1" "subtype5" "subtype3" "subtype5"
 [85] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype5"
 [91] "subtype2" "subtype3" "subtype2" "subtype2" "subtype5" "subtype5"
 [97] "subtype5" "subtype5" "subtype2" "subtype2" "subtype1" "subtype3"
[103] "subtype2" "subtype5" "subtype5"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0         1         0         0         0          0
  subtype2       1        1         3         0         0         1          3
  subtype3       9        3         9         0         1         1          1
  subtype4       4        1         5         0         0         2          0
  subtype5       6        2        13         1         0         2          4
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          3        0         0
  subtype2          5          2        0         3
  subtype3          4          1        2         0
  subtype4          3          3        7         0
  subtype5          6          1        6         2
D6V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  0  5  0
  subtype2  0  2 14  3
  subtype3  1  9 23  0
  subtype4  1  3 20  2
  subtype5  2  9 29  5
D6V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  2  1  3
  subtype2  6  7  6
  subtype3 23  6  3
  subtype4 10  8  8
  subtype5 23 15  6
D6V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1  6  0   0  0
  subtype2 15  1   2  1
  subtype3 26  2   0  4
  subtype4 18  8   0  0
  subtype5 33  7   0  5
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  4  2
  subtype2  7 12
  subtype3 11 22
  subtype4 15 11
  subtype5 23 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    2
  subtype2    7   12
  subtype3   11   22
  subtype4   15   11
  subtype5   23   23
D6V8, binary
          cls
clus        0  1
  subtype1  5  1
  subtype2 16  3
  subtype3 32  1
  subtype4 23  1
  subtype5 41  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    1
  subtype2   16    3
  subtype3   32    1
  subtype4   23    1
  subtype5   41    4
D6V9, binary
          cls
clus        0  1
  subtype1  0  6
  subtype2  2 17
  subtype3  1 32
  subtype4  0 26
  subtype5  2 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    2   17
  subtype3    1   32
  subtype4    0   26
  subtype5    2   44
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  0  0
  subtype2 17  1  0  1
  subtype3 27  0  1  1
  subtype4 18  0  7  0
  subtype5 30  1  4  1
D6V10, multiclass
D6V11, continuous

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 50  7
  subtype2 23  1
  subtype3 40  4
subtype1 subtype2 subtype3 
      57       24       44 
subtype1 subtype2 subtype3 
       7        1        4 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3742 
       24.13        17.23        25.02         8.45        11.67         0.99 
TCGA-AG-4022 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
        0.99         0.20         0.69         0.72         4.60        10.19 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        6.02         9.37        13.97        60.00         7.99        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        32.58         0.49         2.40        19.96 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 
       17.00        15.85        16.34        16.31        11.51        13.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.76         0.46        47.08 

$subtype2
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 
       19.10        14.50        15.35        10.39         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3892 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 
        0.99         1.02         0.49         1.45         1.81         6.02 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6160 TCGA-EI-6506 TCGA-EI-6508 
        6.94         4.70        15.02        30.05        20.55        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 TCGA-G5-6233 TCGA-G5-6235 
       18.28        17.69         8.61        10.78        18.25        55.76 

$subtype3
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3582 
       10.62        13.55        12.72        10.39        12.00         1.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        1.02         1.02         0.99         7.96         0.95         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        1.02         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         1.02        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.94        23.01        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        12.00        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AG-A036 
       38.01        72.07 

subtype1 subtype2 subtype3 
    0.20     0.49     0.92 
subtype1 subtype2 subtype3 
  129.27    55.76    72.07 
subtype1 subtype2 subtype3 
  11.010   10.585   10.800 
[1] "0.2 - 129.3 (11.0)" "0.5 - 55.8 (10.6)"  "0.9 - 72.1 (10.8)" 
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
  [7] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[103] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[115] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[121] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       7        2        14         1         1         0          6
  subtype2       8        0         5         1         1         2          1
  subtype3      15        6        18         0         0         4          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          7         10        3         5
  subtype2          6          0        3         2
  subtype3          9          4        9         0
D7V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  2  9 40  7
  subtype2  2  7 19  3
  subtype3  4 13 45  4
D7V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 26 15 15
  subtype2 16 10  5
  subtype3 40 15 11
D7V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 45  6   1  5
  subtype2 20  3   0  8
  subtype3 56 10   0  0
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1 28 31
  subtype2 12 19
  subtype3 31 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   31
  subtype2   12   19
  subtype3   31   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       12       31
  MALE         31       19       35
D7V8, binary
          cls
clus        0  1
  subtype1 57  2
  subtype2 24  4
  subtype3 57  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57    2
  subtype2   24    4
  subtype3   57    6
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                57       24       57
  RECTAL MUCINOUS ADENOCARCINOMA        2        4        6
D7V9, binary
          cls
clus        0  1
  subtype1  3 56
  subtype2  2 29
  subtype3  1 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   56
  subtype2    2   29
  subtype3    1   65
     clus
vv    subtype1 subtype2 subtype3
  NO         3        2        1
  YES       56       29       65
          vv
clus       R0 R1 R2 RX
  subtype1 41  0  1  4
  subtype2 20  1  1  0
  subtype3 55  1  9  0
D7V10, multiclass
D7V11, continuous

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 41  4
  subtype2  5  0
  subtype3 42  7
  subtype4 25  1
subtype1 subtype2 subtype3 subtype4 
      45        5       49       26 
subtype1 subtype2 subtype3 subtype4 
       4        0        7        1 
$subtype1
TCGA-AF-2692 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       13.55        10.39         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        1.02         0.99         0.99         7.96         0.95         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         1.02        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       40.96        38.01        72.07 

$subtype2
TCGA-AF-3400 TCGA-AG-3575 TCGA-BM-6198 TCGA-EI-6507 TCGA-EI-6917 
       12.72        12.00        10.19        19.96        17.46 

$subtype3
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3742 
       24.13        17.23        25.02         8.45        11.67         0.99 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CL-5917 TCGA-CL-5918 
        0.20         0.69         0.72         4.60        60.00         7.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 
      129.27        24.13        32.58         0.49         2.40        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
       15.85        16.34        16.31        11.51        13.61        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6572 
       47.08 

$subtype4
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-4022 
       10.62        19.10        14.50        15.35        10.39         0.99 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.49         1.45         1.81         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6160 
        9.37         4.70        13.97        11.01        15.02        30.05 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 
       20.55        20.91        18.28        17.69         8.61        10.78 
TCGA-G5-6233 TCGA-G5-6235 
       18.25        55.76 

subtype1 subtype2 subtype3 subtype4 
    0.92    10.19     0.20     0.49 
subtype1 subtype2 subtype3 subtype4 
   72.07    19.96   129.27    55.76 
subtype1 subtype2 subtype3 subtype4 
   6.020   12.720   11.510   10.895 
[1] "0.9 - 72.1 (6.0)"   "10.2 - 20.0 (12.7)" "0.2 - 129.3 (11.5)"
[4] "0.5 - 55.8 (10.9)" 
  [1] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
  [7] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [61] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [67] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [97] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
  [1] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
  [7] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [61] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [67] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [97] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
  [1] "subtype3" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
  [7] "subtype3" "subtype1" "subtype4" "subtype3" "subtype4" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [49] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [55] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
 [61] "subtype4" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [67] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [85] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [97] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[103] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype3"
[109] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1      17        5        17         0         0         4          0
  subtype2       0        1         3         0         0         0          1
  subtype3       5        1        13         1         1         0          4
  subtype4       8        1         4         1         1         2          2
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          9          4       10         0
  subtype2          2          0        0         0
  subtype3          6         10        3         4
  subtype4          5          0        2         3
D8V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  4 15 44  4
  subtype2  0  0  7  0
  subtype3  1  8 34  7
  subtype4  3  6 19  3
D8V4, multiclass
          vv
clus       N0 N1 N2
  subtype1 40 15 12
  subtype2  4  3  0
  subtype3 22 11 15
  subtype4 16 11  4
D8V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 56 11   0  0
  subtype2  6  0   0  0
  subtype3 39  5   1  5
  subtype4 20  3   0  8
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1 30 37
  subtype2  2  5
  subtype3 25 26
  subtype4 14 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   37
  subtype2    2    5
  subtype3   25   26
  subtype4   14   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30        2       25       14
  MALE         37        5       26       17
D8V8, binary
          cls
clus        0  1
  subtype1 58  6
  subtype2  4  2
  subtype3 49  2
  subtype4 27  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    6
  subtype2    4    2
  subtype3   49    2
  subtype4   27    2
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                58        4       49       27
  RECTAL MUCINOUS ADENOCARCINOMA        6        2        2        2
D8V9, binary
          cls
clus        0  1
  subtype1  0 67
  subtype2  2  5
  subtype3  2 49
  subtype4  2 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   67
  subtype2    2    5
  subtype3    2   49
  subtype4    2   29
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        2        2        2
  YES       67        5       49       29
          vv
clus       R0 R1 R2 RX
  subtype1 56  1 10  0
  subtype2  6  0  0  0
  subtype3 36  0  1  4
  subtype4 18  1  0  0
D8V10, multiclass
D8V11, continuous

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 12  4
  subtype2 32  6
  subtype3 15  0
  subtype4 10  0
  subtype5 30  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       38       15       10       32 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        6        0        0        2 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AH-6644 
       24.13        17.23        25.02        10.39        14.50         0.72 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6571 
       12.95         5.29        57.24       129.27        16.31         0.85 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
        2.17         0.66         0.69        47.08 

$subtype2
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-4022 
       19.10        15.35        11.67        10.39         1.02         0.99 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.49         1.45         0.69        10.19         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.70        13.97        60.00        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.99        14.01         6.97        30.05        13.02        10.06 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6509 
       41.33        24.13        51.48        32.58        20.55        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-F5-6811 TCGA-G5-6233 
       18.28        15.85        17.69        16.34         1.02        18.25 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$subtype3
TCGA-AF-5654 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-A00C TCGA-AG-A025 TCGA-CI-6620 
        8.45         0.99         0.99         6.02        49.94         6.02 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EF-5830 
        7.99        15.02        15.02        36.00       126.41         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-F5-6465 
        2.40        20.91         3.39 

$subtype4
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-4001 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
        2.01         1.02         1.02        12.00        12.00        63.98 
TCGA-AG-A036 TCGA-AH-6549 TCGA-EI-6507 TCGA-F5-6810 
       72.07         0.20        19.96         0.39 

$subtype5
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3581 
       17.95        10.62        13.55        12.72        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        0.99         1.02         0.92         1.02         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
        1.02         1.02         1.02        20.94        13.91        17.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       13.02         1.02        70.03        10.98         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X 
       61.94        40.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     0.49     0.49     0.20     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.27    60.00   126.41    72.07    70.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.725   13.495    7.990    7.005    1.480 
[1] "0.7 - 129.3 (13.7)" "0.5 - 60.0 (13.5)"  "0.5 - 126.4 (8.0)" 
[4] "0.2 - 72.1 (7.0)"   "0.9 - 70.0 (1.5)"  
  [1] "subtype1" "subtype5" "subtype1" "subtype5" "subtype5" "subtype2"
  [7] "subtype5" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [13] "subtype2" "subtype2" "subtype5" "subtype5" "subtype5" "subtype4"
 [19] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype5" "subtype5" "subtype4" "subtype5"
 [37] "subtype5" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [43] "subtype5" "subtype5" "subtype4" "subtype4" "subtype5" "subtype4"
 [49] "subtype5" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [55] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [91] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype1" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype2" "subtype1" "subtype2"
  [1] "subtype1" "subtype5" "subtype1" "subtype5" "subtype5" "subtype2"
  [7] "subtype5" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [13] "subtype2" "subtype2" "subtype5" "subtype5" "subtype5" "subtype4"
 [19] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype5" "subtype5" "subtype4" "subtype5"
 [37] "subtype5" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [43] "subtype5" "subtype5" "subtype4" "subtype4" "subtype5" "subtype4"
 [49] "subtype5" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [55] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [91] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype1" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype2" "subtype1" "subtype2"
  [1] "subtype1" "subtype5" "subtype1" "subtype5" "subtype5" "subtype2"
  [7] "subtype5" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [13] "subtype2" "subtype2" "subtype5" "subtype5" "subtype5" "subtype4"
 [19] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype5"
 [25] "subtype2" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [31] "subtype3" "subtype5" "subtype5" "subtype5" "subtype4" "subtype5"
 [37] "subtype5" "subtype2" "subtype5" "subtype5" "subtype3" "subtype5"
 [43] "subtype5" "subtype5" "subtype4" "subtype4" "subtype5" "subtype4"
 [49] "subtype5" "subtype3" "subtype5" "subtype5" "subtype5" "subtype5"
 [55] "subtype4" "subtype2" "subtype2" "subtype4" "subtype2" "subtype1"
 [61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [73] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [79] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [91] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype1"
[103] "subtype1" "subtype4" "subtype2" "subtype1" "subtype1" "subtype2"
[109] "subtype2" "subtype1" "subtype2"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       0        1         4         0         0         0          0
  subtype2       6        1         6         1         1         2          5
  subtype3       6        0         4         1         0         0          0
  subtype4       1        1         3         0         0         1          0
  subtype5      15        5        16         0         0         3          0
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          5        0         3
  subtype2          9          4        3         2
  subtype3          3          0        1         2
  subtype4          1          0        2         0
  subtype5          5          4        8         0
D9V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  0 14  3
  subtype2  2  9 29  2
  subtype3  3  3  9  2
  subtype4  0  2  8  0
  subtype5  4 12 37  3
D9V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  5  4  7
  subtype2 16 19  7
  subtype3 11  4  2
  subtype4  6  1  2
  subtype5 36 10 10
D9V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 11  2   1  3
  subtype2 28  4   0  9
  subtype3 13  2   1  1
  subtype4  7  2   0  1
  subtype5 48  8   0  0
D9V6, multiclass
D9V7, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 18 24
  subtype3 11  6
  subtype4  3  7
  subtype5 26 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   18   24
  subtype3   11    6
  subtype4    3    7
  subtype5   26   30
D9V8, binary
          cls
clus        0  1
  subtype1 15  2
  subtype2 40  1
  subtype3 17  0
  subtype4  9  1
  subtype5 46  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    2
  subtype2   40    1
  subtype3   17    0
  subtype4    9    1
  subtype5   46    6
D9V9, binary
          cls
clus        0  1
  subtype1  2 16
  subtype2  3 39
  subtype3  0 17
  subtype4  0 10
  subtype5  1 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   16
  subtype2    3   39
  subtype3    0   17
  subtype4    0   10
  subtype5    1   55
          vv
clus       R0 R1 R2 RX
  subtype1 12  0  0  1
  subtype2 23  1  1  1
  subtype3 13  0  1  1
  subtype4  7  0  2  1
  subtype5 47  1  7  0
D9V10, multiclass
D9V11, continuous

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 17  1
  subtype2 37  3
  subtype3 45  8
subtype1 subtype2 subtype3 
      18       40       53 
subtype1 subtype2 subtype3 
       1        3        8 
$subtype1
TCGA-AF-2687 TCGA-AF-5654 TCGA-AG-3731 TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-A01Y 
       24.13         8.45         1.02         0.99         1.02        63.98 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DY-A1DD 
        0.20         0.69         6.02         6.02         4.70        57.24 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6513 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6641 
        0.49        20.91        16.34         2.17         0.39        26.43 

$subtype2
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 
       17.95        10.62        13.55        12.72        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.99         7.96         0.95         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
       20.94        13.91         6.02        17.03        13.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        12.00        70.03        10.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       38.93        61.94        40.96        72.07 

$subtype3
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       17.23        19.10        25.02        14.50        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3742 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       10.39         0.99         0.99         0.49         1.45         0.72 
TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.94         9.37        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        14.01        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         6.97        30.05        12.95        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.41        41.33       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       32.58         2.40        20.55        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       15.85        17.69        16.31         3.39         0.85         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.69        18.25        55.76        47.08 

subtype1 subtype2 subtype3 
    0.20     0.92     0.49 
subtype1 subtype2 subtype3 
   63.98    72.07   129.27 
subtype1 subtype2 subtype3 
    5.36     6.99    14.01 
[1] "0.2 - 64.0 (5.4)"   "0.9 - 72.1 (7.0)"   "0.5 - 129.3 (14.0)"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
  [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [13] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
 [61] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
 [67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [73] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [79] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [97] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype3" "subtype1"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       2        1         3         1         0         0          1
  subtype2      17        5        15         0         0         4          0
  subtype3       9        2        15         1         1         2          4
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          2        3         2
  subtype2          8          4       10         0
  subtype3          8          7        1         5
D10V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  2 16  1
  subtype2  5 14 42  3
  subtype3  3 10 39  6
D10V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  7  9  3
  subtype2 38 14 12
  subtype3 29 15 13
D10V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1 13  5   0  2
  subtype2 53 11   0  0
  subtype3 41  2   2 12
D10V6, multiclass
D10V7, binary
          cls
clus        0  1
  subtype1  9 11
  subtype2 29 35
  subtype3 28 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   11
  subtype2   29   35
  subtype3   28   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       29       28
  MALE         11       35       31
D10V8, binary
          cls
clus        0  1
  subtype1 19  1
  subtype2 52  8
  subtype3 56  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    1
  subtype2   52    8
  subtype3   56    1
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                19       52       56
  RECTAL MUCINOUS ADENOCARCINOMA        1        8        1
D10V9, binary
          cls
clus        0  1
  subtype1  1 19
  subtype2  1 63
  subtype3  4 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   19
  subtype2    1   63
  subtype3    4   55
     clus
vv    subtype1 subtype2 subtype3
  NO         1        1        4
  YES       19       63       55
          vv
clus       R0 R1 R2 RX
  subtype1 13  0  2  1
  subtype2 53  1  9  0
  subtype3 36  1  0  3
D10V10, multiclass
D10V11, continuous

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1  9  2
  subtype2 16  4
  subtype3 20  1
  subtype4 14  2
subtype1 subtype2 subtype3 subtype4 
      11       20       21       16 
subtype1 subtype2 subtype3 subtype4 
       2        4        1        2 
$subtype1
TCGA-AF-2687 TCGA-AF-5654 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       24.13         8.45         1.02         0.20         6.02         6.02 
TCGA-CL-4957 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EI-6507 
       13.97        13.02        41.33        32.58        19.96 

$subtype2
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6644 TCGA-DC-6681 
       17.23        25.02        14.50         0.99         0.72        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6514 
       10.06         5.29        57.24       129.27        24.13        16.31 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-G5-6572 
        0.69        47.08 

$subtype3
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6547 
       19.10        15.35        11.67        10.39         0.49         1.45 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 
        0.69        10.19         6.94         9.37         4.70        10.98 
TCGA-DC-4749 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       11.01        20.55        17.00        18.28        15.85        17.69 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.25        55.76        26.43 

$subtype4
TCGA-AG-3742 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        0.99        60.00         7.99        15.02        12.99        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DG 
       15.02        36.00         6.97        30.05       126.41        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6513 
        0.49         2.40        20.91        16.34 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.39     0.49     0.49 
subtype1 subtype2 subtype3 subtype4 
   41.33   129.27    55.76   126.41 
subtype1 subtype2 subtype3 subtype4 
  13.020    7.675   11.670   15.020 
[1] "0.2 - 41.3 (13.0)"  "0.4 - 129.3 (7.7)"  "0.5 - 55.8 (11.7)" 
[4] "0.5 - 126.4 (15.0)"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[67] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[67] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype2"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype2" "subtype2" "subtype4" "subtype1" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[67] "subtype2" "subtype3"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0         3         0         0         1          2
  subtype2       0        2         7         0         0         0          0
  subtype3       4        0         2         1         1         1          2
  subtype4       6        0         4         1         0         0          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          0          1        2         1
  subtype2          2          5        1         3
  subtype3          6          2        1         1
  subtype4          3          1        0         2
D11V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  0  2 10  0
  subtype2  0  0 18  3
  subtype3  2  5 14  2
  subtype4  2  5  9  2
D11V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  4  6  1
  subtype2  9  3  8
  subtype3  9  9  5
  subtype4 11  5  2
D11V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1  7  3   0  2
  subtype2 15  2   1  3
  subtype3 14  1   0  7
  subtype4 14  1   1  2
D11V6, multiclass
D11V7, binary
          cls
clus        0  1
  subtype1  5  7
  subtype2 12 10
  subtype3  9 14
  subtype4  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    7
  subtype2   12   10
  subtype3    9   14
  subtype4    8   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        5       12        9        8
  MALE          7       10       14       10
D11V8, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2 20  1
  subtype3 21  1
  subtype4 18  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2   20    1
  subtype3   21    1
  subtype4   18    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                12       20       21       18
  RECTAL MUCINOUS ADENOCARCINOMA        0        1        1        0
D11V9, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2  1 21
  subtype3  3 20
  subtype4  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2    1   21
  subtype3    3   20
  subtype4    0   18
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        3        0
  YES       11       21       20       18
          vv
clus       R0 R1 R2 RX
  subtype1  4  0  1  1
  subtype2 13  0  1  1
  subtype3 14  1  0  0
  subtype4 14  0  0  2
D11V10, multiclass
D11V11, continuous

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1  8  0
  subtype2 15  3
  subtype3 13  0
  subtype4  8  2
  subtype5 15  4
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       18       13       10       19 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        3        0        2        4 
$subtype1
TCGA-AF-5654 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6160 TCGA-DC-6682 
        8.45        13.97        15.02        12.99        30.05        13.02 
TCGA-EI-6506 TCGA-EI-6510 
       20.55        18.28 

$subtype2
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6547 TCGA-AH-6644 
       17.23        25.02        14.50         0.99         1.45         0.72 
TCGA-DC-4745 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE 
       10.98        12.95        10.06         5.29        57.24       129.27 
TCGA-DY-A1DF TCGA-EI-6514 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       24.13        16.31         0.85         1.02         0.66         0.69 

$subtype3
TCGA-AF-2687 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       24.13         1.02         0.20         6.02         6.02         4.70 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6513 TCGA-F5-6702 TCGA-F5-6810 
        0.49        19.96        20.91        16.34         2.17         0.39 
TCGA-G5-6641 
       26.43 

$subtype4
TCGA-AG-3742 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        0.99        60.00         7.99        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-EF-5831 TCGA-F5-6465 TCGA-G5-6572 
        6.97         2.40         3.39        47.08 

$subtype5
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6643 
       19.10        15.35        11.67        10.39         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-DC-4749 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.19         6.94         9.37        11.01       126.41        41.33 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-G5-6233 
       51.48        32.58        17.00        15.85        17.69        18.25 
TCGA-G5-6235 
       55.76 

subtype1 subtype2 subtype3 subtype4 subtype5 
    8.45     0.66     0.20     0.99     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 
   30.05   129.27    26.43    60.00   126.41 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.495   10.520    6.020   11.000   15.850 
[1] "8.4 - 30.1 (14.5)"  "0.7 - 129.3 (10.5)" "0.2 - 26.4 (6.0)"  
[4] "1.0 - 60.0 (11.0)"  "0.5 - 126.4 (15.8)"
 [1] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype3" "subtype4" "subtype2"
[13] "subtype5" "subtype2" "subtype3" "subtype5" "subtype2" "subtype5"
[19] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype2" "subtype5" "subtype1" "subtype1"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype5" "subtype5" "subtype2"
[43] "subtype2" "subtype2" "subtype5" "subtype5" "subtype3" "subtype4"
[49] "subtype1" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype3" "subtype2" "subtype4" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype5" "subtype5"
[67] "subtype4" "subtype3"
 [1] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype3" "subtype4" "subtype2"
[13] "subtype5" "subtype2" "subtype3" "subtype5" "subtype2" "subtype5"
[19] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype2" "subtype5" "subtype1" "subtype1"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype5" "subtype5" "subtype2"
[43] "subtype2" "subtype2" "subtype5" "subtype5" "subtype3" "subtype4"
[49] "subtype1" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype3" "subtype2" "subtype4" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype5" "subtype5"
[67] "subtype4" "subtype3"
 [1] "subtype3" "subtype2" "subtype5" "subtype2" "subtype2" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype3" "subtype4" "subtype2"
[13] "subtype5" "subtype2" "subtype3" "subtype5" "subtype2" "subtype5"
[19] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[25] "subtype4" "subtype4" "subtype2" "subtype5" "subtype1" "subtype1"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype2" "subtype5" "subtype5" "subtype2"
[43] "subtype2" "subtype2" "subtype5" "subtype5" "subtype3" "subtype4"
[49] "subtype1" "subtype3" "subtype3" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype3" "subtype2" "subtype4" "subtype2" "subtype3"
[61] "subtype3" "subtype2" "subtype2" "subtype2" "subtype5" "subtype5"
[67] "subtype4" "subtype3"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       3        0         2         0         0         1          1
  subtype2       1        2         5         0         0         0          0
  subtype3       1        0         2         1         0         0          1
  subtype4       3        0         3         0         0         0          1
  subtype5       3        0         4         1         1         1          2
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          0        0         1
  subtype2          3          5        0         2
  subtype3          2          1        3         2
  subtype4          0          1        0         1
  subtype5          5          2        1         1
D12V3, multiclass
          vv
clus       T1 T2 T3 T4
  subtype1  1  3  5  0
  subtype2  0  1 16  3
  subtype3  1  1 11  1
  subtype4  1  3  4  1
  subtype5  1  4 15  2
D12V4, multiclass
          vv
clus       N0 N1 N2
  subtype1  6  3  0
  subtype2  9  3  7
  subtype3  4  7  2
  subtype4  6  1  2
  subtype5  8  9  5
D12V5, multiclass
          vv
clus       M0 M1 M1A MX
  subtype1  7  0   0  2
  subtype2 15  0   1  4
  subtype3  7  5   0  2
  subtype4  6  0   1  2
  subtype5 15  2   0  4
D12V6, multiclass
D12V7, binary
          cls
clus        0  1
  subtype1  5  4
  subtype2 13  7
  subtype3  4 10
  subtype4  5  5
  subtype5  7 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    4
  subtype2   13    7
  subtype3    4   10
  subtype4    5    5
  subtype5    7   15
D12V8, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 18  1
  subtype3 13  1
  subtype4 10  0
  subtype5 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   18    1
  subtype3   13    1
  subtype4   10    0
  subtype5   21    0
D12V9, binary
          cls
clus        0  1
  subtype1  0  9
  subtype2  1 19
  subtype3  1 13
  subtype4  0 10
  subtype5  3 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    1   19
  subtype3    1   13
  subtype4    0   10
  subtype5    3   19
          vv
clus       R0 R1 R2 RX
  subtype1  7  0  0  0
  subtype2 12  0  0  1
  subtype3  8  0  2  1
  subtype4  7  0  0  2
  subtype5 11  1  0  0
D12V10, multiclass
D12V11, continuous
> q(save="no")
