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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/PAAD-TP/4468382/PAAD-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/PAAD-TP/4434820/PAAD-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=PAAD-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=PAAD-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/PAAD-TP/4434820/PAAD-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/PAAD-TP/4468382/PAAD-TP.mergedcluster.txt"

nPatients in clinical file=53, in cluster file=66, common to both=53
[1]  8 53
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5 
 9 31  5  6  1 
 1  2  3  4 
 9 31  5  6 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
17 24 12 
 1  2  3 
17 24 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
17 11 12 10 
 1  2  3  4 
17 11 12 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 5 19 26 
 1  2  3 
 5 19 26 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
25 11 17 
 1  2  3 
25 11 17 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
11 19 23 
 1  2  3 
11 19 23 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
21  9 23 
 1  2  3 
21  9 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
12 22 19 
 1  2  3 
12 22 19 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 53 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
          NA          303          360           NA          153          158 
TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7289 
           4            7            1          392          232          239 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
          28           20           NA            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
         366            8           19           30           21           NA 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 
          28           15            3            5           NA           90 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-IB-7644 
          23           31           NA          182           46          347 
TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          NA           NA           NA           NA           NA          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
         851           NA           NA           NA           NA           NA 
TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
         488           NA           NA           17          521 
Variable 1:'AGE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "YEAROFTOBACCOSMOKINGONSET" "COMPLETENESS.OF.RESECTION"
[11] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 53 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=32, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 2  3 46  2 
[1] "table(vv)"
vv
T1+T2 T3+T4 
    5    48 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 2  3 46  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 5

$Class1_nSamples
[1] 48

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
    5    48 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=11, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=11, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  5  4
  subtype2 19 10
  subtype3  2  3
  subtype4  5  0
subtype1 subtype2 subtype3 subtype4 
       9       29        5        5 
subtype1 subtype2 subtype3 subtype4 
       4       10        3        0 
$subtype1
TCGA-F2-6879 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8005 TCGA-IB-7646 
       10.98         7.86         0.92         0.13         3.91         4.77 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 
       15.65         4.04        17.13 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 
        9.96        11.84         7.07         5.03         5.19         0.13 
TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
        7.63         0.26        12.13         0.26         0.62         0.99 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
        0.69         0.92         0.49         0.10         2.96         0.76 
TCGA-HZ-A49H TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
        1.02        49.38        21.86        15.35        19.82        27.98 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.78        16.04        15.95         0.56 

$subtype3
TCGA-FB-A545 TCGA-H6-8124 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
        0.03        12.89         3.58        19.66         3.85 

$subtype4
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7644 
        0.66        12.03         0.16         1.51        11.41 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.10     0.03     0.16 
subtype1 subtype2 subtype3 subtype4 
   17.13    49.38    19.66    12.03 
subtype1 subtype2 subtype3 subtype4 
    4.77     5.19     3.85     1.51 
[1] "0.1 - 17.1 (4.8)" "0.1 - 49.4 (5.2)" "0.0 - 19.7 (3.9)" "0.2 - 12.0 (1.5)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype4" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
[31] "subtype4" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype4" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
[31] "subtype4" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2" "subtype1" "subtype1"
[13] "subtype4" "subtype1" "subtype2" "subtype2" "subtype4" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
[31] "subtype4" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        0         0         9         0        0
  subtype2        2        1         5        21         2        0
  subtype3        0        1         1         3         0        0
  subtype4        0        0         0         4         0        2
D1V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     0     9
  subtype2     4    27
  subtype3     1     4
  subtype4     0     6
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1+T2        0        4        1        0
  T3+T4        9       27        4        6
D1V5, binary
          cls
clus        0  1
  subtype1  0  9
  subtype2  9 22
  subtype3  2  3
  subtype4  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    9   22
  subtype3    2    3
  subtype4    1    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        0        9        2        1
  1        9       22        3        5
          vv
clus       M0 M1 MX
  subtype1  6  0  3
  subtype2 15  0 16
  subtype3  5  0  0
  subtype4  1  2  3
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  2  7
  subtype2 20 11
  subtype3  3  2
  subtype4  3  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2   20   11
  subtype3    3    2
  subtype4    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2       20        3        3
  MALE          7       11        2        3
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                   7
  subtype2                                  28
  subtype3                                   5
  subtype4                                   5
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     2
  subtype3                                     0
  subtype4                                     1
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                0
  subtype4                                                0
D1V8, multiclass
D1V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        8        2        1 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[8] "subtype2"
D1V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        6        1        1 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       R0 R1 RX
  subtype1  3  5  1
  subtype2 21  8  1
  subtype3  3  1  0
  subtype4  1  5  0
D1V11, multiclass
D1V12, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  5
  subtype2 17  5
  subtype3  5  7
subtype1 subtype2 subtype3 
      16       22       12 
subtype1 subtype2 subtype3 
       5        5        7 
$subtype1
TCGA-F2-6879 TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 
       10.98         0.03        12.89         7.86         0.66         0.13 
TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7652 
       12.03         0.92         0.16         1.51        11.41        15.65 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 
        4.04         3.58        19.66         3.85 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 
        9.96        11.84         7.07         5.19         0.13         0.23 
TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 
        7.63         0.92         0.26        12.13         0.99         0.69 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-IB-7649 
        0.49         0.10         2.96         0.76         1.02        15.35 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       27.98        16.04        15.95         0.56 

$subtype3
TCGA-F2-A44G TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8005 TCGA-HZ-A4BH TCGA-IB-7645 
        5.03         0.26         0.62         3.91         5.98        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-8127 
        4.77        21.86        19.82        43.79        15.78        17.13 

subtype1 subtype2 subtype3 
    0.03     0.10     0.26 
subtype1 subtype2 subtype3 
   19.66    27.98    49.38 
subtype1 subtype2 subtype3 
   3.945    1.990   10.880 
[1] "0.0 - 19.7 (3.9)"  "0.1 - 28.0 (2.0)"  "0.3 - 49.4 (10.9)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[19] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[37] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[49] "subtype2" "subtype3"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         2        12         0        2
  subtype2        2        1         3        17         1        0
  subtype3        0        0         1        10         1        0
D2V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     1    16
  subtype2     4    20
  subtype3     0    12
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        1        4        0
  T3+T4       16       20       12
D2V5, binary
          cls
clus        0  1
  subtype1  4 13
  subtype2  6 18
  subtype3  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   13
  subtype2    6   18
  subtype3    2   10
   clus
vv  subtype1 subtype2 subtype3
  0        4        6        2
  1       13       18       10
          vv
clus       M0 M1 MX
  subtype1  9  2  6
  subtype2 10  0 14
  subtype3  8  0  4
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1  9  8
  subtype2 13 11
  subtype3  6  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    8
  subtype2   13   11
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       13        6
  MALE          8       11        6
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  14
  subtype2                                  21
  subtype3                                  12
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     2
  subtype2                                     2
  subtype3                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                0
D2V8, multiclass
D2V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        8        2 
 [1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
D2V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        6        2 
[1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[8] "subtype2" "subtype2"
          vv
clus       R0 R1 RX
  subtype1  6  9  1
  subtype2 17  5  0
  subtype3  5  6  1
D2V11, multiclass
D2V12, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 10  7
  subtype2  8  3
  subtype3  5  5
  subtype4  8  1
subtype1 subtype2 subtype3 subtype4 
      17       11       10        9 
subtype1 subtype2 subtype3 subtype4 
       7        3        5        1 
$subtype1
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7919 TCGA-HZ-7922 
       10.98         5.03         0.03        12.89         0.66         0.13 
TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7646 TCGA-IB-7651 
       12.03         0.92         0.16         1.51         4.77        19.82 
TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
        4.04         3.58        19.66         3.85        17.13 

$subtype2
TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-HZ-7918 TCGA-HZ-8002 TCGA-HZ-A49G 
       11.84         5.19         0.23         0.92         0.99         0.76 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-8126 
       15.35        15.65        15.78        16.04         0.56 

$subtype3
TCGA-F2-7276 TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8519 
        7.07         0.13         7.63         0.62         0.69         0.10 
TCGA-HZ-A4BH TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 
        5.98        21.86        43.79        15.95 

$subtype4
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8317 TCGA-HZ-8638 TCGA-HZ-A49H 
        0.26        12.13         0.26         0.49         2.96         1.02 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7885 
       11.41        49.38        27.98 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.23     0.10     0.26 
subtype1 subtype2 subtype3 subtype4 
   19.82    16.04    43.79    49.38 
subtype1 subtype2 subtype3 subtype4 
   4.040    5.190    6.525    2.960 
[1] "0.0 - 19.8 (4.0)" "0.2 - 16.0 (5.2)" "0.1 - 43.8 (6.5)" "0.3 - 49.4 (3.0)"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype4" "subtype3" "subtype1"
[25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
[31] "subtype4" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype4" "subtype3" "subtype1"
[25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
[31] "subtype4" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype4" "subtype4" "subtype1" "subtype4" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype4" "subtype3" "subtype1"
[25] "subtype4" "subtype2" "subtype4" "subtype3" "subtype1" "subtype4"
[31] "subtype4" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype4" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[43] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        0        1         2        13         0        1
  subtype2        0        0         1         9         1        0
  subtype3        1        1         1         8         1        0
  subtype4        1        0         2         6         0        1
D3V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     1    16
  subtype2     1    10
  subtype3     2    10
  subtype4     1     9
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1+T2        1        1        2        1
  T3+T4       16       10       10        9
D3V5, binary
          cls
clus        0  1
  subtype1  4 13
  subtype2  1 10
  subtype3  4  8
  subtype4  3  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   13
  subtype2    1   10
  subtype3    4    8
  subtype4    3    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        4        1        4        3
  1       13       10        8        7
          vv
clus       M0 M1 MX
  subtype1 12  1  4
  subtype2  8  0  3
  subtype3  4  0  8
  subtype4  2  1  7
D3V6, multiclass
D3V7, binary
          cls
clus       0 1
  subtype1 9 8
  subtype2 5 6
  subtype3 7 5
  subtype4 7 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    8
  subtype2    5    6
  subtype3    7    5
  subtype4    7    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9        5        7        7
  MALE          8        6        5        3
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  15
  subtype2                                  11
  subtype3                                  10
  subtype4                                   9
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     0
  subtype3                                     2
  subtype4                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                0
  subtype4                                                1
D3V8, multiclass
D3V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        4        2        2 
[1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[8] "subtype2" "subtype1"
D3V10, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       4        4        1        2 
[1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[8] "subtype1"
          vv
clus       R0 R1 RX
  subtype1  7  9  0
  subtype2  5  5  0
  subtype3  9  2  0
  subtype4  6  3  1
D3V11, multiclass
D3V12, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5  0
  subtype2 11  7
  subtype3 15  9
subtype1 subtype2 subtype3 
       5       18       24 
subtype1 subtype2 subtype3 
       0        7        9 
$subtype1
TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8317 TCGA-HZ-8638 TCGA-HZ-A4BK 
       12.13         0.26         0.49         2.96         1.51 

$subtype2
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7919 TCGA-HZ-7922 
       10.98         5.03         0.03        12.89         0.66         0.13 
TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7651 
       12.03         0.92         0.16        11.41         4.77        19.82 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
       27.98         4.04         3.58        19.66         3.85        17.13 

$subtype3
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-H6-A45N 
       11.84         7.07         5.19         0.13         0.23         7.63 
TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8519 
        0.92         0.26         0.62         0.99         0.69         0.10 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 
        0.76         1.02         5.98        49.38        21.86        15.35 
TCGA-IB-7652 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 
       15.65        43.79        15.78        16.04        15.95         0.56 

subtype1 subtype2 subtype3 
    0.26     0.03     0.10 
subtype1 subtype2 subtype3 
   12.13    27.98    49.38 
subtype1 subtype2 subtype3 
   1.510    4.900    5.585 
[1] "0.3 - 12.1 (1.5)" "0.0 - 28.0 (4.9)" "0.1 - 49.4 (5.6)"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        0         1         3         0        0
  subtype2        0        1         2        14         0        2
  subtype3        1        1         3        19         2        0
D4V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     1     4
  subtype2     1    18
  subtype3     3    23
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        1        1        3
  T3+T4        4       18       23
D4V5, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2  4 15
  subtype3  6 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2    4   15
  subtype3    6   20
   clus
vv  subtype1 subtype2 subtype3
  0        2        4        6
  1        3       15       20
          vv
clus       M0 M1 MX
  subtype1  0  0  5
  subtype2 13  2  4
  subtype3 13  0 13
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 11  8
  subtype3 14 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   11    8
  subtype3   14   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3       11       14
  MALE          2        8       12
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                   3
  subtype2                                  18
  subtype3                                  24
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     1
  subtype2                                     0
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
D4V8, multiclass
D4V9, continuous
D4V10, continuous
          vv
clus       R0 R1 RX
  subtype1  2  2  1
  subtype2  8 10  0
  subtype3 17  7  0
D4V11, multiclass
D4V12, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 16  8
  subtype2  9  2
  subtype3  8  7
subtype1 subtype2 subtype3 
      24       11       15 
subtype1 subtype2 subtype3 
       8        2        7 
$subtype1
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 
       10.98         5.03         0.03        12.89         7.86         0.66 
TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-8315 
        0.13        12.13        12.03         0.26         3.91         0.92 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7651 
        0.16         2.96         1.51        11.41         4.77        19.82 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
       27.98         4.04         3.58        19.66         3.85        17.13 

$subtype2
TCGA-F2-6880 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-HZ-7918 TCGA-HZ-8002 TCGA-HZ-8317 
        9.96         5.19         0.23         0.92         0.99         0.49 
TCGA-HZ-A49G TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 
        0.76        15.35        15.65        15.78        16.04 

$subtype3
TCGA-F2-7273 TCGA-F2-7276 TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8001 
       11.84         7.07         0.13         7.63         0.26         0.62 
TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 
        0.69         0.10         1.02         5.98        49.38        21.86 
TCGA-IB-7888 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.95         0.56 

subtype1 subtype2 subtype3 
    0.03     0.23     0.10 
subtype1 subtype2 subtype3 
   27.98    16.04    49.38 
subtype1 subtype2 subtype3 
   4.405    5.190    5.980 
[1] "0.0 - 28.0 (4.4)" "0.2 - 16.0 (5.2)" "0.1 - 49.4 (6.0)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
D5V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         3        18         0        2
  subtype2        0        0         1        10         0        0
  subtype3        1        1         2        11         2        0
D5V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     2    23
  subtype2     1    10
  subtype3     2    15
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        1        2
  T3+T4       23       10       15
D5V5, binary
          cls
clus        0  1
  subtype1  6 19
  subtype2  1 10
  subtype3  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   19
  subtype2    1   10
  subtype3    5   12
   clus
vv  subtype1 subtype2 subtype3
  0        6        1        5
  1       19       10       12
          vv
clus       M0 M1 MX
  subtype1 13  2 10
  subtype2  7  0  4
  subtype3  7  0 10
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1 13 12
  subtype2  5  6
  subtype3 10  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   12
  subtype2    5    6
  subtype3   10    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13        5       10
  MALE         12        6        7
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  21
  subtype2                                  11
  subtype3                                  15
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     2
  subtype2                                     0
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
D5V8, multiclass
D5V9, continuous
D5V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       6        3        2 
[1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[8] "subtype2" "subtype1"
          vv
clus       R0 R1 RX
  subtype1 10 12  2
  subtype2  6  4  0
  subtype3 12  4  0
D5V11, multiclass
D5V12, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  4  5
  subtype2 14  5
  subtype3 15  7
subtype1 subtype2 subtype3 
       9       19       22 
subtype1 subtype2 subtype3 
       5        5        7 
$subtype1
TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8519 TCGA-HZ-A4BH TCGA-IB-7645 
        0.13         7.63         0.26         0.10         5.98        49.38 
TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 
       21.86        43.79        15.95 

$subtype2
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-HZ-7918 
        9.96        11.84         7.07         5.19         0.23         0.92 
TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G 
        0.13         0.26         0.99         0.69         0.49         0.76 
TCGA-HZ-A49H TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 
        1.02        15.35        19.82        15.65        15.78        16.04 
TCGA-IB-8126 
        0.56 

$subtype3
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 
       10.98         5.03         0.03        12.89         7.86         0.66 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 
       12.13        12.03         0.62         3.91         0.92         0.16 
TCGA-HZ-8638 TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 
        2.96         1.51        11.41         4.77        27.98         4.04 
TCGA-IB-7887 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
        3.58        19.66         3.85        17.13 

subtype1 subtype2 subtype3 
    0.10     0.13     0.03 
subtype1 subtype2 subtype3 
   49.38    19.82    27.98 
subtype1 subtype2 subtype3 
   7.630    1.020    4.405 
[1] "0.1 - 49.4 (7.6)" "0.1 - 19.8 (1.0)" "0.0 - 28.0 (4.4)"
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[19] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype3"
D6V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         2         7         0        0
  subtype2        0        0         1        17         1        0
  subtype3        1        1         3        15         1        2
D6V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     2     9
  subtype2     1    18
  subtype3     2    21
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        1        2
  T3+T4        9       18       21
D6V5, binary
          cls
clus        0  1
  subtype1  4  7
  subtype2  1 18
  subtype3  7 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    7
  subtype2    1   18
  subtype3    7   16
   clus
vv  subtype1 subtype2 subtype3
  0        4        1        7
  1        7       18       16
          vv
clus       M0 M1 MX
  subtype1  4  0  7
  subtype2 11  0  8
  subtype3 12  2  9
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  7  4
  subtype2 10  9
  subtype3 11 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    4
  subtype2   10    9
  subtype3   11   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       10       11
  MALE          4        9       12
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                   9
  subtype2                                  19
  subtype3                                  19
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     2
  subtype2                                     0
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                0
  subtype3                                                1
D6V8, multiclass
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        6 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
D6V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        5        5 
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3"
          vv
clus       R0 R1 RX
  subtype1  8  2  0
  subtype2 11  6  1
  subtype3  9 12  1
D6V11, multiclass
D6V12, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 13  7
  subtype2  8  1
  subtype3 12  9
subtype1 subtype2 subtype3 
      20        9       21 
subtype1 subtype2 subtype3 
       7        1        9 
$subtype1
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 
       10.98         5.03         0.03        12.89         7.86         0.66 
TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A4BK 
       12.03         3.91         0.92         0.16         2.96         1.51 
TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7890 
       11.41         4.77        27.98         4.04         3.58        19.66 
TCGA-IB-7893 TCGA-IB-8127 
        3.85        17.13 

$subtype2
TCGA-F2-6880 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8317 
        9.96         0.92         0.13        12.13         0.26         0.49 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 
       19.82        15.65        16.04 

$subtype3
TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-H6-A45N 
       11.84         7.07         5.19         0.13         0.23         7.63 
TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8519 TCGA-HZ-A49G 
        0.26         0.62         0.99         0.69         0.10         0.76 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7888 
        1.02         5.98        49.38        21.86        15.35        43.79 
TCGA-IB-7889 TCGA-IB-7897 TCGA-IB-8126 
       15.78        15.95         0.56 

subtype1 subtype2 subtype3 
    0.03     0.13     0.10 
subtype1 subtype2 subtype3 
   27.98    19.82    49.38 
subtype1 subtype2 subtype3 
   4.405    9.960    5.190 
[1] "0.0 - 28.0 (4.4)"  "0.1 - 19.8 (10.0)" "0.1 - 49.4 (5.2)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
[49] "subtype3" "subtype1"
D7V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         2        15         0        2
  subtype2        0        0         1         8         0        0
  subtype3        1        1         3        16         2        0
D7V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     2    19
  subtype2     0     9
  subtype3     3    20
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        0        3
  T3+T4       19        9       20
D7V5, binary
          cls
clus        0  1
  subtype1  5 16
  subtype2  1  8
  subtype3  6 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   16
  subtype2    1    8
  subtype3    6   17
   clus
vv  subtype1 subtype2 subtype3
  0        5        1        6
  1       16        8       17
          vv
clus       M0 M1 MX
  subtype1 12  2  7
  subtype2  5  0  4
  subtype3 10  0 13
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1 10 11
  subtype2  5  4
  subtype3 13 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   11
  subtype2    5    4
  subtype3   13   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10        5       13
  MALE         11        4       10
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  17
  subtype2                                   9
  subtype3                                  21
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     2
  subtype2                                     0
  subtype3                                     2
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
D7V8, multiclass
D7V9, continuous
D7V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       5        2        4 
[1] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[8] "subtype3" "subtype1"
          vv
clus       R0 R1 RX
  subtype1  7 12  1
  subtype2  6  2  1
  subtype3 15  6  0
D7V11, multiclass
D7V12, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  5  5
  subtype2 14  7
  subtype3 14  5
subtype1 subtype2 subtype3 
      10       21       19 
subtype1 subtype2 subtype3 
       5        7        5 
$subtype1
TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-8001 TCGA-HZ-8519 TCGA-HZ-A4BH 
        0.13         7.63         0.26         0.62         0.10         5.98 
TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7888 TCGA-IB-7897 
       49.38        21.86        43.79        15.95 

$subtype2
TCGA-F2-6879 TCGA-F2-A44G TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 
       10.98         5.03         0.03        12.89         7.86         0.66 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-8638 
       12.13        12.03         3.91         0.92         0.16         2.96 
TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
        1.51        11.41         4.77        27.98         4.04         3.58 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 
       19.66         3.85        17.13 

$subtype3
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44H TCGA-FB-A4P6 TCGA-HZ-7918 
        9.96        11.84         7.07         5.19         0.23         0.92 
TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-A49G 
        0.13         0.26         0.99         0.69         0.49         0.76 
TCGA-HZ-A49H TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7889 TCGA-IB-7891 
        1.02        15.35        19.82        15.65        15.78        16.04 
TCGA-IB-8126 
        0.56 

subtype1 subtype2 subtype3 
    0.10     0.03     0.13 
subtype1 subtype2 subtype3 
   49.38    27.98    19.82 
subtype1 subtype2 subtype3 
   6.805    4.770    1.020 
[1] "0.1 - 49.4 (6.8)" "0.0 - 28.0 (4.8)" "0.1 - 19.8 (1.0)"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype3" "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[49] "subtype3" "subtype2"
D8V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  subtype1        1        1         2         7         1        0
  subtype2        1        1         3        15         0        2
  subtype3        0        0         1        17         1        0
D8V3, multiclass
          vv
clus       T1+T2 T3+T4
  subtype1     2    10
  subtype2     2    20
  subtype3     1    18
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        2        1
  T3+T4       10       20       18
D8V5, binary
          cls
clus        0  1
  subtype1  5  7
  subtype2  6 16
  subtype3  1 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    7
  subtype2    6   16
  subtype3    1   18
   clus
vv  subtype1 subtype2 subtype3
  0        5        6        1
  1        7       16       18
          vv
clus       M0 M1 MX
  subtype1  4  0  8
  subtype2 12  2  8
  subtype3 11  0  8
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1  7  5
  subtype2 11 11
  subtype3 10  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2   11   11
  subtype3   10    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       11       10
  MALE          5       11        9
          vv
clus       PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  subtype1                                  10
  subtype2                                  18
  subtype3                                  19
          vv
clus       PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  subtype1                                     2
  subtype2                                     2
  subtype3                                     0
          vv
clus       PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  subtype1                                                0
  subtype2                                                1
  subtype3                                                0
D8V8, multiclass
D8V9, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        6 
 [1] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
D8V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        5        5 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype3" "subtype2"
          vv
clus       R0 R1 RX
  subtype1  9  2  0
  subtype2  8 12  1
  subtype3 11  6  1
D8V11, multiclass
D8V12, continuous
> q(save="no")
