
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/READ-TP/3536846/READ-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/3352996/READ-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=336, 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 
 7 32 46 55 22 
 1  2  3  4  5 
 7 32 46 55 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  4  5  6  7 
10 12  7  7  4  7  4 
 1  2  3  4  5  6  7 
10 12  7  7  4  7  4 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
19 12 20 
 1  2  3 
19 12 20 
[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 
15 19 27 14 
 1  2  3  4 
15 19 27 14 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 9 13  8 22 23 
 1  2  3  4  5 
 9 13  8 22 23 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 166 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         594          482          358          323          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-4110 TCGA-AF-5654 
         387          536          316          264          441          257 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
         231          193          223           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          304          153 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
         273          224          212          849          212          608 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
         180          121          152            8         3635         1257 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        1741         3683          734         1566          991           15 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
          73          232            5           66          250           14 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
         121           20          210          216          187          108 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         121           83          159          237           84           62 
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         1451           NA          636 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=96,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "DISTANT.METASTASIS"                    
 [6] "LYMPH.NODE.METASTASIS"                 
 [7] "COMPLETENESS.OF.RESECTION"             
 [8] "NUMBER.OF.LYMPH.NODES"                 
 [9] "TUMOR.STAGECODE"                       
[10] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1  T2  T3  T4 T4A T4B 
  9  30 112   5   8   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 166 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE

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 
       15.85        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
D1V3, 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
D1V4, 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
D1V5, 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       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
          vv
clus       N0 N1 N1A N2
  subtype1 16  5   0  4
  subtype2 16  4   0  2
  subtype3 10  5   1  6
D1V7, multiclass
          vv
clus       R0 R1 R2
  subtype1 22  0  3
  subtype2 19  0  2
  subtype3 16  1  5
D1V8, multiclass
D1V9, continuous
D1V10, 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
D1V11, multiclass

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 
       15.85        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
D2V3, 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
D2V4, 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
D2V5, 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       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
          vv
clus       N0 N1 N1A N2
  subtype1 16  4   0  4
  subtype2 15  8   1  5
  subtype3 11  2   0  3
D2V7, multiclass
          vv
clus       R0 R1 R2
  subtype1 21  0  3
  subtype2 22  1  5
  subtype3 14  0  2
D2V8, multiclass
D2V9, continuous
D2V10, 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
D2V11, multiclass

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  7  0
  subtype2 20  4
  subtype3 31  3
  subtype4 46  1
  subtype5 15  3
subtype1 subtype2 subtype3 subtype4 subtype5 
       7       24       34       47       18 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        4        3        1        3 
$subtype1
TCGA-AF-2687 TCGA-AG-A00Y TCGA-CI-6623 TCGA-DY-A1DE TCGA-F5-6810 TCGA-F5-6812 
       19.53        23.01         9.37       121.08         0.39         0.66 
TCGA-F5-6813 
        0.69 

$subtype2
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-4001 
       15.85        10.39         1.02         0.99         0.99         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A026 TCGA-DC-4745 
        1.02         1.02         1.02        12.00         1.94        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DG 
       11.01         5.03         8.98        27.91         5.00        51.48 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-G5-6572 
        3.98         6.90         7.10         2.76         1.02        47.08 

$subtype3
TCGA-AF-2690 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3605 
       11.77         6.35         7.33         1.02         1.02         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A023 
        1.02         0.92        15.91         1.02        63.98        51.98 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CL-5917 
       40.96         0.49         0.69         0.72         6.02        60.00 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.99         7.36         6.97         3.98       119.51        41.33 
TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6883 TCGA-EI-6885 TCGA-F5-6465 
       57.24         0.49         8.22         3.98         5.23         3.39 
TCGA-F5-6702 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6641 
        2.17         0.76         0.46        20.91 

$subtype4
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3581 
       10.62        13.55        12.72         8.45        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 
        2.01         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01W 
        1.02         0.99        20.94        13.91        17.03        70.03 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       10.98        49.94        61.94         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 
       10.19         6.02         6.94         4.70        13.97         9.99 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       19.99         5.92         0.26        32.58         2.40         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6884 
        0.16         2.17         0.46         0.66         3.55         2.73 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
        7.79         2.04         0.53         1.08        47.70 

$subtype5
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3896 TCGA-AG-3999 
       19.10        17.62        14.50         7.59         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A02G 
        0.99         6.02        25.94        13.02        12.00        38.93 
TCGA-AG-A032 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6881 TCGA-F5-6571 TCGA-G5-6233 
       38.01         6.97        24.13         6.15         0.85        18.25 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.39     0.99     0.46     0.16     0.85 
subtype1 subtype2 subtype3 subtype4 subtype5 
  121.08    51.48   119.51    70.03    38.93 
subtype1 subtype2 subtype3 subtype4 subtype5 
   9.370    5.015    5.625    5.920   12.510 
[1] "0.4 - 121.1 (9.4)" "1.0 - 51.5 (5.0)"  "0.5 - 119.5 (5.6)"
[4] "0.2 - 70.0 (5.9)"  "0.8 - 38.9 (12.5)"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype5"
  [7] "subtype4" "subtype5" "subtype2" "subtype5" "subtype4" "subtype5"
 [13] "subtype3" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype4" "subtype4" "subtype5" "subtype5"
 [43] "subtype1" "subtype4" "subtype3" "subtype5" "subtype2" "subtype3"
 [49] "subtype5" "subtype2" "subtype4" "subtype3" "subtype4" "subtype3"
 [55] "subtype4" "subtype2" "subtype5" "subtype4" "subtype3" "subtype5"
 [61] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [67] "subtype4" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [79] "subtype2" "subtype2" "subtype3" "subtype5" "subtype2" "subtype3"
 [85] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[103] "subtype4" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[109] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[115] "subtype4" "subtype3" "subtype5" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[127] "subtype5" "subtype4" "subtype2" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype5"
  [7] "subtype4" "subtype5" "subtype2" "subtype5" "subtype4" "subtype5"
 [13] "subtype3" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype4" "subtype4" "subtype5" "subtype5"
 [43] "subtype1" "subtype4" "subtype3" "subtype5" "subtype2" "subtype3"
 [49] "subtype5" "subtype2" "subtype4" "subtype3" "subtype4" "subtype3"
 [55] "subtype4" "subtype2" "subtype5" "subtype4" "subtype3" "subtype5"
 [61] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [67] "subtype4" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [79] "subtype2" "subtype2" "subtype3" "subtype5" "subtype2" "subtype3"
 [85] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[103] "subtype4" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[109] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[115] "subtype4" "subtype3" "subtype5" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[127] "subtype5" "subtype4" "subtype2" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype4" "subtype5"
  [7] "subtype4" "subtype5" "subtype2" "subtype5" "subtype4" "subtype5"
 [13] "subtype3" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [19] "subtype3" "subtype3" "subtype4" "subtype3" "subtype4" "subtype4"
 [25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype3" "subtype4"
 [31] "subtype2" "subtype4" "subtype5" "subtype5" "subtype2" "subtype2"
 [37] "subtype2" "subtype5" "subtype4" "subtype4" "subtype5" "subtype5"
 [43] "subtype1" "subtype4" "subtype3" "subtype5" "subtype2" "subtype3"
 [49] "subtype5" "subtype2" "subtype4" "subtype3" "subtype4" "subtype3"
 [55] "subtype4" "subtype2" "subtype5" "subtype4" "subtype3" "subtype5"
 [61] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [67] "subtype4" "subtype3" "subtype4" "subtype4" "subtype1" "subtype4"
 [73] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
 [79] "subtype2" "subtype2" "subtype3" "subtype5" "subtype2" "subtype3"
 [85] "subtype4" "subtype4" "subtype3" "subtype2" "subtype4" "subtype3"
 [91] "subtype3" "subtype3" "subtype1" "subtype5" "subtype2" "subtype4"
 [97] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[103] "subtype4" "subtype2" "subtype4" "subtype2" "subtype2" "subtype5"
[109] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[115] "subtype4" "subtype3" "subtype5" "subtype3" "subtype1" "subtype2"
[121] "subtype1" "subtype1" "subtype4" "subtype4" "subtype3" "subtype3"
[127] "subtype5" "subtype4" "subtype2" "subtype3"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  1  6
  subtype2 15 17
  subtype3 22 24
  subtype4 26 29
  subtype5 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2   15   17
  subtype3   22   24
  subtype4   26   29
  subtype5   10   12
D3V4, binary
          cls
clus        0  1
  subtype1  7  0
  subtype2 32  0
  subtype3 40  4
  subtype4 44  9
  subtype5 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   32    0
  subtype3   40    4
  subtype4   44    9
  subtype5   20    0
D3V5, binary
          cls
clus        0  1
  subtype1  1  6
  subtype2  0 32
  subtype3  1 45
  subtype4  2 53
  subtype5  2 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    0   32
  subtype3    1   45
  subtype4    2   53
  subtype5    2   20
          vv
clus       M0 M1 M1A MX
  subtype1  7  0   0  0
  subtype2 22  9   0  0
  subtype3 34  7   0  5
  subtype4 45  4   1  4
  subtype5 15  2   1  4
D3V6, multiclass
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1  5  0   0   0   0  2   0   0  0
  subtype2 14  8   3   1   0  4   0   1  0
  subtype3 23  8   0   2   1  7   1   3  1
  subtype4 34 13   1   1   0  4   1   1  0
  subtype5  7  6   0   1   0  6   0   2  0
D3V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1  5  0  0  0
  subtype2 24  1  4  0
  subtype3 32  0  4  2
  subtype4 43  1  3  1
  subtype5 17  0  1  0
D3V8, multiclass
D3V9, continuous
D3V10, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       1        0         4         0         0         0          0
  subtype2       4        1         8         0         0         0          0
  subtype3       6        2        13         1         1         1          3
  subtype4      16        4        10         1         0         3          5
  subtype5       3        1         3         0         1         1          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          0          2        0         0
  subtype2          9          0        6         2
  subtype3          3          6        6         1
  subtype4          6          2        3         4
  subtype5          5          3        2         2
D3V11, multiclass

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 24  1
  subtype2 33  3
  subtype3 23  4
subtype1 subtype2 subtype3 
      25       36       27 
subtype1 subtype2 subtype3 
       1        3        4 
$subtype1
TCGA-AF-2687 TCGA-AF-3911 TCGA-AG-4022 TCGA-AG-A01Y TCGA-AH-6549 TCGA-AH-6897 
       19.53        17.62         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         5.03         8.98         6.97        27.91 
TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6513 
        6.97       119.51        57.24       121.08         0.49         6.90 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6864 
        5.23         2.76         3.39         2.17         0.39         0.46 
TCGA-G5-6641 
       20.91 

$subtype2
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       11.77        19.10        14.50         7.59         6.35         7.33 
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         7.36        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
        5.92         3.98        41.33        32.58         7.63         0.16 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6571 
        8.22         3.98         6.15         2.73         7.79         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        47.70        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         9.99 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6508 
        5.00         0.26        24.13        51.48         2.40         2.17 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-7004 
        0.46         0.66         7.10         3.55         3.98         2.04 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        1.02         0.53        18.25 

subtype1 subtype2 subtype3 
    0.20     0.16     0.26 
subtype1 subtype2 subtype3 
  121.08    60.00    72.07 
subtype1 subtype2 subtype3 
   6.020    7.475    3.550 
[1] "0.2 - 121.1 (6.0)" "0.2 - 60.0 (7.5)"  "0.3 - 72.1 (3.5)" 
 [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
D4V3, 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
D4V4, 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
D4V5, 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       M0 M1 M1A MX
  subtype1 16  5   1  3
  subtype2 27  1   1  8
  subtype3 24  4   0  3
D4V6, multiclass
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1 11  4   1   1   1  4   0   2  1
  subtype2 14 12   1   3   0  3   2   3  0
  subtype3 16  5   1   1   0  5   0   2  1
D4V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 18  0  0  0
  subtype2 25  1  0  1
  subtype3 21  1  2  2
D4V8, multiclass
D4V9, continuous
D4V10, 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          4        1         2
  subtype3          3          2        2         4
D4V11, multiclass

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 22  1
  subtype2 34  3
  subtype3 38  7
subtype1 subtype2 subtype3 
      23       37       45 
subtype1 subtype2 subtype3 
       1        3        7 
$subtype1
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3599 
       15.85        11.77        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 
        9.99         6.97         5.92         5.00         0.26         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         8.68         6.35         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        19.99         3.98 
TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       41.33         7.63         0.16         3.98         6.90         6.15 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        7.79         3.39         0.85         1.08         0.46        18.25 
TCGA-G5-6235 
       47.70 

$subtype3
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.45         7.59         7.33         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 
        5.03         7.36        27.91       119.51        57.24       121.08 
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         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 
        8.22         0.46         0.66         7.10         3.55         2.73 
TCGA-EI-6885 TCGA-F5-6810 TCGA-G5-6641 
        5.23         0.39        20.91 

subtype1 subtype2 subtype3 
    0.26     0.16     0.20 
subtype1 subtype2 subtype3 
   47.08    72.07   121.08 
subtype1 subtype2 subtype3 
    1.02     7.63     7.10 
[1] "0.3 - 47.1 (1.0)"  "0.2 - 72.1 (7.6)"  "0.2 - 121.1 (7.1)"
  [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
D5V3, 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
D5V4, 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
D5V5, 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       M0 M1 M1A MX
  subtype1 24  6   2  0
  subtype2 34  3   0  5
  subtype3 40  9   0  5
D5V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2A N2B NX
  subtype1 14  6   0   1  8   2   1  0
  subtype2 25 10   1   0  4   1   1  1
  subtype3 25 13   3   3  7   0   2  1
D5V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 24  0  5  1
  subtype2 36  1  1  1
  subtype3 37  1  6  0
D5V8, multiclass
D5V9, continuous
D5V10, 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          5        5         3
  subtype2          7          2        2         0
  subtype3          8          2        8         2
D5V11, multiclass

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  1
  subtype2 17  0
  subtype3 26  2
  subtype4 12  1
  subtype5 36  7
subtype1 subtype2 subtype3 subtype4 subtype5 
       4       17       28       13       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        0        2        1        7 
$subtype1
TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-F5-6864 
       24.13         2.17         8.22         0.46 

$subtype2
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3914 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-A036 
       11.77        12.72         8.68         6.35         1.02        72.07 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6917 
        6.97         5.92         5.00         0.26         0.16         7.79 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
        0.85         2.17         1.08         0.76        47.70 

$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         9.99 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6513 
        6.97        19.99        41.33         7.63         3.98         6.90 
TCGA-EI-6881 TCGA-EI-6882 TCGA-F5-6465 TCGA-G5-6233 
        6.15         3.55         3.39        18.25 

$subtype4
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3727 
       15.85        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         7.59         7.33         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         5.03         7.36        27.91 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
        3.98       119.51        57.24       121.08        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         0.46         0.66         7.10         2.73 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
        5.23         0.39         1.02         0.66         0.69        47.08 
TCGA-G5-6641 
       20.91 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.16     0.69     0.95     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
   24.13    72.07    70.03    15.85   121.08 
subtype1 subtype2 subtype3 subtype4 subtype5 
   5.195    5.920    8.990    1.020    6.020 
[1] "0.5 - 24.1 (5.2)"  "0.2 - 72.1 (5.9)"  "0.7 - 70.0 (9.0)" 
[4] "0.9 - 15.8 (1.0)"  "0.2 - 121.1 (6.0)"
  [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
D6V3, 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
D6V4, 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
D6V5, 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       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
          vv
clus       N0 N1 N1A N1B N2 N2A N2B NX
  subtype1  2  0   1   0  2   0   1  0
  subtype2  6  6   0   1  2   3   1  0
  subtype3 23  6   0   0  2   0   1  1
  subtype4 10  7   1   0  8   0   0  0
  subtype5 23 10   2   3  5   0   1  1
D6V7, multiclass
          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  0
D6V8, multiclass
D6V9, continuous
D6V10, 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          1        0         3
  subtype3          4          1        2         0
  subtype4          3          3        7         0
  subtype5          6          1        6         2
D6V11, multiclass

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 10  0
  subtype2 10  0
  subtype3  7  0
  subtype4  5  2
  subtype5  4  0
  subtype6  7  0
  subtype7  4  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      10       10        7        7        4        7        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       0        0        0        2        0        0        0 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AH-6644 TCGA-DC-6156 TCGA-DC-6158 TCGA-EI-6885 
       19.53        11.77         0.72         6.97         6.97         5.23 
TCGA-EI-6917 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        7.79         0.85         2.17         1.02 

$subtype2
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-4022 TCGA-CI-6624 
       19.10        17.62        14.50         7.59         0.99         4.70 
TCGA-DC-6160 TCGA-EI-6884 TCGA-EI-7004 TCGA-G5-6235 
       19.99         2.73         2.04        47.70 

$subtype3
TCGA-AF-5654 TCGA-AH-6549 TCGA-AH-6897 TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-5869 
        8.45         0.20         4.60         9.37         9.99         5.03 
TCGA-F5-6810 
        0.39 

$subtype4
TCGA-AG-3742 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6154 TCGA-DY-A1DF TCGA-DY-A1H8 
        0.99        60.00         7.99         8.98        24.13        32.58 
TCGA-EF-5830 
        0.49 

$subtype5
TCGA-AH-6643 TCGA-DT-5265 TCGA-F5-6814 TCGA-F5-6861 
        0.69         0.26         0.53         1.08 

$subtype6
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-EI-6883 TCGA-EI-7002 
       27.91         3.98         5.00       119.51         3.98         2.76 
TCGA-F5-6813 
        0.69 

$subtype7
TCGA-DY-A1DE TCGA-F5-6812 TCGA-F5-6863 TCGA-F5-6864 
      121.08         0.66         0.76         0.46 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.72     0.99     0.20     0.49     0.26     0.69     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   19.53    47.70     9.99    60.00     1.08   119.51   121.08 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   6.100   11.045    5.030    8.980    0.610    3.980    0.710 
[1] "0.7 - 19.5 (6.1)"  "1.0 - 47.7 (11.0)" "0.2 - 10.0 (5.0)" 
[4] "0.5 - 60.0 (9.0)"  "0.3 - 1.1 (0.6)"   "0.7 - 119.5 (4.0)"
[7] "0.5 - 121.1 (0.7)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype4" "subtype2" "subtype3" "subtype5" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype1" "subtype6" "subtype1" "subtype2"
[25] "subtype6" "subtype6" "subtype5" "subtype6" "subtype7" "subtype4"
[31] "subtype4" "subtype4" "subtype6" "subtype2" "subtype1" "subtype1"
[37] "subtype6" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[43] "subtype7" "subtype6" "subtype5" "subtype5" "subtype7" "subtype7"
[49] "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype4" "subtype2" "subtype3" "subtype5" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype1" "subtype6" "subtype1" "subtype2"
[25] "subtype6" "subtype6" "subtype5" "subtype6" "subtype7" "subtype4"
[31] "subtype4" "subtype4" "subtype6" "subtype2" "subtype1" "subtype1"
[37] "subtype6" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[43] "subtype7" "subtype6" "subtype5" "subtype5" "subtype7" "subtype7"
[49] "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype4" "subtype2" "subtype3" "subtype5" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
[19] "subtype3" "subtype4" "subtype1" "subtype6" "subtype1" "subtype2"
[25] "subtype6" "subtype6" "subtype5" "subtype6" "subtype7" "subtype4"
[31] "subtype4" "subtype4" "subtype6" "subtype2" "subtype1" "subtype1"
[37] "subtype6" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[43] "subtype7" "subtype6" "subtype5" "subtype5" "subtype7" "subtype7"
[49] "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus       0 1
  subtype1 4 6
  subtype2 6 6
  subtype3 2 5
  subtype4 6 1
  subtype5 1 3
  subtype6 1 6
  subtype7 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    6    6
  subtype3    2    5
  subtype4    6    1
  subtype5    1    3
  subtype6    1    6
  subtype7    3    1
D7V4, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2  9  1
  subtype3  7  0
  subtype4  7  0
  subtype5  3  1
  subtype6  7  0
  subtype7  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2    9    1
  subtype3    7    0
  subtype4    7    0
  subtype5    3    1
  subtype6    7    0
  subtype7    4    0
D7V5, binary
          cls
clus        0  1
  subtype1  1  9
  subtype2  2 10
  subtype3  0  7
  subtype4  0  7
  subtype5  0  4
  subtype6  0  7
  subtype7  0  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    2   10
  subtype3    0    7
  subtype4    0    7
  subtype5    0    4
  subtype6    0    7
  subtype7    0    4
          vv
clus       M0 M1 M1A MX
  subtype1  6  2   1  1
  subtype2  7  0   0  5
  subtype3  6  0   0  1
  subtype4  4  1   0  2
  subtype5  4  0   0  0
  subtype6  6  1   0  0
  subtype7  4  0   0  0
D7V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2B NX
  subtype1  3  2   0   1  2   1  1
  subtype2  6  2   0   1  1   2  0
  subtype3  5  0   1   0  0   0  1
  subtype4  3  1   0   0  2   1  0
  subtype5  3  0   0   0  0   1  0
  subtype6  4  0   0   1  2   0  0
  subtype7  2  1   0   0  1   0  0
D7V7, multiclass
          vv
clus       R0 R1 RX
  subtype1  8  0  0
  subtype2  7  1  0
  subtype3  5  0  0
  subtype4  3  0  2
  subtype5  3  0  1
  subtype6  6  0  0
  subtype7  3  0  0
D7V8, multiclass
D7V9, continuous
D7V10, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE IIIA STAGE IIIB
  subtype1       1        0         2         0         0          1          0
  subtype2       4        1         1         0         0          1          2
  subtype3       4        0         1         0         0          0          1
  subtype4       1        0         1         1         0          1          0
  subtype5       0        1         1         0         0          1          0
  subtype6       1        0         2         0         1          0          1
  subtype7       0        0         2         0         0          0          1
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          1        1         2
  subtype2          1        0         2
  subtype3          0        0         0
  subtype4          2        0         1
  subtype5          1        0         0
  subtype6          1        1         0
  subtype7          1        0         0
D7V11, multiclass

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 18  1
  subtype2 10  0
  subtype3 19  1
subtype1 subtype2 subtype3 
      19       10       20 
subtype1 subtype2 subtype3 
       1        0        1 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6156 TCGA-DT-5265 
       19.53        11.77         0.69         0.72         6.97         0.26 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
      121.08        24.13         5.23         7.79         2.04         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 
        2.17         0.39         0.66         0.69         0.53         0.76 
TCGA-F5-6864 
        0.46 

$subtype2
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-4022 TCGA-CI-6624 
       19.10        17.62        14.50         7.59         0.99         4.70 
TCGA-DC-6158 TCGA-DC-6160 TCGA-EI-6884 TCGA-G5-6235 
        6.97        19.99         2.73        47.70 

$subtype3
TCGA-AF-5654 TCGA-AG-3742 TCGA-AH-6549 TCGA-AH-6897 TCGA-CI-6623 TCGA-CL-5917 
        8.45         0.99         0.20         4.60         9.37        60.00 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 
        7.99         9.99         5.03         8.98        27.91         3.98 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6883 TCGA-EI-7002 
        5.00       119.51        32.58         0.49         3.98         2.76 
TCGA-F5-6811 TCGA-F5-6861 
        1.02         1.08 

subtype1 subtype2 subtype3 
    0.26     0.99     0.20 
subtype1 subtype2 subtype3 
  121.08    47.70   119.51 
subtype1 subtype2 subtype3 
   0.850   11.045    5.015 
[1] "0.3 - 121.1 (0.8)" "1.0 - 47.7 (11.0)" "0.2 - 119.5 (5.0)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[49] "subtype2"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  8 11
  subtype2  5  7
  subtype3 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   11
  subtype2    5    7
  subtype3   10   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        5       10
  MALE         11        7       10
D8V4, binary
          cls
clus        0  1
  subtype1 17  2
  subtype2 10  0
  subtype3 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    2
  subtype2   10    0
  subtype3   20    0
                                clus
vv                               subtype1 subtype2 subtype3
  RECTAL ADENOCARCINOMA                17       10       20
  RECTAL MUCINOUS ADENOCARCINOMA        2        0        0
D8V5, binary
          cls
clus        0  1
  subtype1  1 18
  subtype2  2 10
  subtype3  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   18
  subtype2    2   10
  subtype3    0   20
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        0
  YES       18       10       20
          vv
clus       M0 M1 M1A MX
  subtype1 15  2   1  1
  subtype2  7  0   0  5
  subtype3 15  2   0  3
D8V6, multiclass
          vv
clus       N0 N1 N1A N1B N2 N2B NX
  subtype1  6  3   0   1  5   3  1
  subtype2  7  2   0   1  1   1  0
  subtype3 13  1   1   1  2   1  1
D8V7, multiclass
          vv
clus       R0 R1 RX
  subtype1 15  0  1
  subtype2  7  1  0
  subtype3 13  0  2
D8V8, multiclass
D8V9, continuous
D8V10, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE IIIA STAGE IIIB
  subtype1       0        1         5         0         0          1          1
  subtype2       5        1         1         0         0          1          2
  subtype3       6        0         4         1         1          2          2
          vv
clus       STAGE IIIC STAGE IV STAGE IVA
  subtype1          5        1         3
  subtype2          1        0         1
  subtype3          1        1         1
D8V11, multiclass

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 13  3
  subtype2 33  5
  subtype3 15  0
  subtype4 10  0
  subtype5 30  2
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       38       15       10       32 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        5        0        0        2 
$subtype1
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AH-6644 
       19.53        11.77        17.62        10.39        14.50         0.72 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6514 TCGA-F5-6571 
        5.92         0.26        57.24       121.08         7.10         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         7.59         6.35         7.33         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 
        5.03         7.36         6.97        19.99         3.98         5.00 
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         7.63         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-F5-6811 TCGA-G5-6233 
        0.46         3.98         0.66         6.90         1.02        18.25 
TCGA-G5-6235 TCGA-G5-6641 
       47.70        20.91 

$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         9.99         6.97        27.91       119.51         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-F5-6465 
        2.40         2.17         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         0.16         0.39 

$subtype5
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3581 
       15.85        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 
    0.26     0.46     0.49     0.16     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  121.08    60.00   119.51    72.07    70.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
   8.745    7.345    6.020    1.515    1.480 
[1] "0.3 - 121.1 (8.7)" "0.5 - 60.0 (7.3)"  "0.5 - 119.5 (6.0)"
[4] "0.2 - 72.1 (1.5)"  "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
D9V3, 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
D9V4, 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
D9V5, 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       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
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1  5  3   1   0   0  4   2   1  1
  subtype2 16 13   2   3   1  4   0   3  0
  subtype3 11  3   1   0   0  1   0   1  0
  subtype4  6  1   0   0   0  2   0   0  1
  subtype5 36 10   0   0   0 10   0   0  0
D9V7, multiclass
          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  0
  subtype5 47  1  7  0
D9V8, multiclass
D9V9, continuous
D9V10, 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          4        0         3
  subtype2          9          4        3         2
  subtype3          3          0        1         2
  subtype4          1          0        2         0
  subtype5          5          4        8         0
D9V11, multiclass

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 17  1
  subtype2 37  3
  subtype3 47  6
subtype1 subtype2 subtype3 
      18       40       53 
subtype1 subtype2 subtype3 
       1        3        6 
$subtype1
TCGA-AF-2687 TCGA-AF-5654 TCGA-AG-3731 TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-A01Y 
       19.53         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         2.17         6.90         2.17         0.39        20.91 

$subtype2
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 
       15.85        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 
       11.77        19.10        17.62        14.50         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3742 TCGA-AG-4022 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
        7.33         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         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26       119.51        41.33       121.08        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         7.63         0.16         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
        3.98         0.66         7.10         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        47.70        47.08 

subtype1 subtype2 subtype3 
    0.20     0.92     0.16 
subtype1 subtype2 subtype3 
   63.98    72.07   121.08 
subtype1 subtype2 subtype3 
   3.435    6.990    7.360 
[1] "0.2 - 64.0 (3.4)"  "0.9 - 72.1 (7.0)"  "0.2 - 121.1 (7.4)"
  [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
D10V3, 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
D10V4, 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
D10V5, 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       M0 M1 M1A MX
  subtype1 13  5   0  2
  subtype2 53 11   0  0
  subtype3 41  2   2 12
D10V6, multiclass
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1  7  7   1   0   1  2   0   1  1
  subtype2 38 13   1   0   0 12   0   0  0
  subtype3 29 10   2   3   0  7   2   4  1
D10V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 13  0  2  0
  subtype2 53  1  9  0
  subtype3 36  1  0  3
D10V8, multiclass
D10V9, continuous
D10V10, 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          6        1         5
D10V11, multiclass

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 14  0
  subtype2 15  3
  subtype3 20  4
  subtype4 12  0
subtype1 subtype2 subtype3 subtype4 
      14       18       24       12 
subtype1 subtype2 subtype3 subtype4 
       0        3        4        0 
$subtype1
TCGA-AF-2687 TCGA-AF-5654 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       19.53         8.45         1.02         0.20         6.02         6.02 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-6160 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 
       13.97        60.00        19.99         3.98         0.26         0.16 
TCGA-EI-6513 TCGA-F5-6702 
        6.90         2.17 

$subtype2
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6644 TCGA-DC-6681 
       11.77        17.62        14.50         0.99         0.72         5.92 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6514 TCGA-F5-6465 
        5.00        57.24       121.08        24.13         7.10         3.39 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6572 
        0.85         0.39         1.02         0.66         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         7.59         6.35         7.33         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-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6509 
       11.01        41.33        51.48        32.58         7.63         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.46         3.98         0.66        18.25        47.70        20.91 

$subtype4
TCGA-AG-3742 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        0.99         7.99         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
       27.91         6.97       119.51         0.49         2.40         2.17 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.39     0.46     0.49 
subtype1 subtype2 subtype3 subtype4 
   60.00   121.08    51.48   119.51 
subtype1 subtype2 subtype3 subtype4 
   6.020    5.460    7.925    6.970 
[1] "0.2 - 60.0 (6.0)"  "0.4 - 121.1 (5.5)" "0.5 - 51.5 (7.9)" 
[4] "0.5 - 119.5 (7.0)"
 [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] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype4" "subtype3" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[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] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype4" "subtype3" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[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] "subtype1" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype4" "subtype3" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
[49] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[67] "subtype2" "subtype3"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1  4 11
  subtype2 11  8
  subtype3 11 16
  subtype4  8  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   11
  subtype2   11    8
  subtype3   11   16
  subtype4    8    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       11       11        8
  MALE         11        8       16        6
D11V4, binary
          cls
clus        0  1
  subtype1 14  1
  subtype2 18  0
  subtype3 25  1
  subtype4 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    1
  subtype2   18    0
  subtype3   25    1
  subtype4   14    0
                                clus
vv                               subtype1 subtype2 subtype3 subtype4
  RECTAL ADENOCARCINOMA                14       18       25       14
  RECTAL MUCINOUS ADENOCARCINOMA        1        0        1        0
D11V5, binary
          cls
clus        0  1
  subtype1  1 14
  subtype2  1 18
  subtype3  3 24
  subtype4  0 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   14
  subtype2    1   18
  subtype3    3   24
  subtype4    0   14
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        3        0
  YES       14       18       24       14
          vv
clus       M0 M1 M1A MX
  subtype1  8  4   0  3
  subtype2 14  0   1  3
  subtype3 17  2   0  7
  subtype4 11  1   1  1
D11V6, multiclass
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1  5  6   0   0   1  2   0   0  1
  subtype2  8  1   0   1   0  4   2   1  1
  subtype3 11  9   1   1   0  2   0   3  0
  subtype4  9  0   2   1   0  1   0   1  0
D11V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1  7  0  1  2
  subtype2 12  0  0  0
  subtype3 15  1  0  0
  subtype4 11  0  1  1
D11V8, multiclass
D11V9, continuous
D11V10, continuous
          vv
clus       STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  subtype1       2        1         2         0         0         1          1
  subtype2       0        1         7         0         0         0          0
  subtype3       4        0         4         1         1         1          3
  subtype4       5        0         3         1         0         0          1
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          2        2         2
  subtype2          2          4        0         2
  subtype3          6          2        1         2
  subtype4          2          0        1         1
D11V11, multiclass

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1  8  0
  subtype2 13  0
  subtype3  7  0
  subtype4 17  3
  subtype5 16  4
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       13        7       20       20 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        0        0        3        4 
$subtype1
TCGA-AF-5654 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6160 TCGA-DC-6682 
        8.45        13.97         9.99         5.03        19.99         3.98 
TCGA-EI-6506 TCGA-EI-6510 
        7.63         0.46 

$subtype2
TCGA-AF-2687 TCGA-AG-3731 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       19.53         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         0.16         2.17         6.90         2.17         0.39 
TCGA-G5-6641 
       20.91 

$subtype3
TCGA-AG-3742 TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        0.99         7.99         7.36         6.97        27.91         6.97 
TCGA-EF-5831 
        2.40 

$subtype4
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AG-4022 TCGA-AH-6547 TCGA-AH-6644 
       11.77        17.62        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         5.92         5.00         0.26        57.24       121.08 
TCGA-DY-A1DF TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       24.13         7.10         3.39         0.85         1.02         0.66 
TCGA-F5-6813 TCGA-G5-6572 
        0.69        47.08 

$subtype5
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AH-6544 TCGA-AH-6643 
       19.10         7.59         6.35         7.33         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DY-A0XA 
       10.19         6.94         9.37        60.00        11.01       119.51 
TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
       41.33        51.48        32.58         8.22         3.98         0.66 
TCGA-G5-6233 TCGA-G5-6235 
       18.25        47.70 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.16     0.99     0.26     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 
   19.99    20.91    27.91   121.08   119.51 
subtype1 subtype2 subtype3 subtype4 subtype5 
    8.04     2.17     6.97     5.46     9.78 
[1] "0.5 - 20.0 (8.0)"  "0.2 - 20.9 (2.2)"  "1.0 - 27.9 (7.0)" 
[4] "0.3 - 121.1 (5.5)" "0.5 - 119.5 (9.8)"
 [1] "subtype2" "subtype4" "subtype5" "subtype4" "subtype4" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype2" "subtype3" "subtype4"
[13] "subtype5" "subtype4" "subtype2" "subtype5" "subtype4" "subtype5"
[19] "subtype2" "subtype2" "subtype5" "subtype5" "subtype2" "subtype1"
[25] "subtype5" "subtype3" "subtype4" "subtype5" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[37] "subtype1" "subtype4" "subtype4" "subtype5" "subtype5" "subtype4"
[43] "subtype4" "subtype4" "subtype5" "subtype5" "subtype2" "subtype3"
[49] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[61] "subtype2" "subtype4" "subtype4" "subtype4" "subtype5" "subtype5"
[67] "subtype4" "subtype2"
 [1] "subtype2" "subtype4" "subtype5" "subtype4" "subtype4" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype2" "subtype3" "subtype4"
[13] "subtype5" "subtype4" "subtype2" "subtype5" "subtype4" "subtype5"
[19] "subtype2" "subtype2" "subtype5" "subtype5" "subtype2" "subtype1"
[25] "subtype5" "subtype3" "subtype4" "subtype5" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[37] "subtype1" "subtype4" "subtype4" "subtype5" "subtype5" "subtype4"
[43] "subtype4" "subtype4" "subtype5" "subtype5" "subtype2" "subtype3"
[49] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[61] "subtype2" "subtype4" "subtype4" "subtype4" "subtype5" "subtype5"
[67] "subtype4" "subtype2"
 [1] "subtype2" "subtype4" "subtype5" "subtype4" "subtype4" "subtype1"
 [7] "subtype5" "subtype5" "subtype5" "subtype2" "subtype3" "subtype4"
[13] "subtype5" "subtype4" "subtype2" "subtype5" "subtype4" "subtype5"
[19] "subtype2" "subtype2" "subtype5" "subtype5" "subtype2" "subtype1"
[25] "subtype5" "subtype3" "subtype4" "subtype5" "subtype1" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[37] "subtype1" "subtype4" "subtype4" "subtype5" "subtype5" "subtype4"
[43] "subtype4" "subtype4" "subtype5" "subtype5" "subtype2" "subtype3"
[49] "subtype1" "subtype2" "subtype2" "subtype5" "subtype1" "subtype5"
[55] "subtype5" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[61] "subtype2" "subtype4" "subtype4" "subtype4" "subtype5" "subtype5"
[67] "subtype4" "subtype2"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1  5  4
  subtype2  3 10
  subtype3  4  4
  subtype4 14  8
  subtype5  8 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    4
  subtype2    3   10
  subtype3    4    4
  subtype4   14    8
  subtype5    8   15
D12V4, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 12  1
  subtype3  8  0
  subtype4 20  1
  subtype5 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   12    1
  subtype3    8    0
  subtype4   20    1
  subtype5   22    0
D12V5, binary
          cls
clus        0  1
  subtype1  0  9
  subtype2  1 12
  subtype3  0  8
  subtype4  1 21
  subtype5  3 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    1   12
  subtype3    0    8
  subtype4    1   21
  subtype5    3   20
          vv
clus       M0 M1 M1A MX
  subtype1  7  0   0  2
  subtype2  7  4   0  2
  subtype3  5  1   1  1
  subtype4 16  0   1  4
  subtype5 15  2   0  5
D12V6, multiclass
          vv
clus       N0 N1 N1A N1B N1C N2 N2A N2B NX
  subtype1  6  2   1   0   0  0   0   0  0
  subtype2  4  5   1   0   1  1   0   0  1
  subtype3  5  0   0   1   0  1   0   1  0
  subtype4 10  1   1   1   0  4   2   1  1
  subtype5  8  8   0   1   0  3   0   3  0
D12V7, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1  7  0  0  0
  subtype2  8  0  1  0
  subtype3  6  0  1  1
  subtype4 13  0  0  1
  subtype5 11  1  0  1
D12V8, multiclass
D12V9, continuous
D12V10, 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        0         2         1         0         0          1
  subtype3       3        0         2         0         0         0          1
  subtype4       1        2         6         0         0         0          0
  subtype5       3        0         4         1         1         1          2
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          0        0         1
  subtype2          2          1        2         2
  subtype3          0          0        1         1
  subtype4          3          4        0         2
  subtype5          5          3        1         1
D12V11, multiclass
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V6 
                    "DISTANT.METASTASIS" 
                                      V7 
                 "LYMPH.NODE.METASTASIS" 
                                      V8 
             "COMPLETENESS.OF.RESECTION" 
                                      V9 
                 "NUMBER.OF.LYMPH.NODES" 
                                     V10 
                       "TUMOR.STAGECODE" 
                                     V11 
                 "NEOPLASM.DISEASESTAGE" 
> q(save="no")
