
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.75.4002/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.75.4002/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/2283023/1.GDAC_mergedClustering.Finished/KIRP-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/2172511/1.GDAC_clinicalDataPicker.Finished/KIRP-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-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=103, in cluster file=103, common to both=101
[1]   8 101
[1] "MRNA_CNMF"
[1] 3
1 2 
7 9 
1 2 
7 9 
[1] "MRNA_CHIERARCHICAL"
[1] 3
1 2 3 
4 7 5 
1 2 3 
4 7 5 
[1] "CN_CNMF"
[1] 3
 1  2  3 
27 54 20 
 1  2  3 
27 54 20 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
21 26 38 
 1  2  3 
21 26 38 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
22 18 12 11 
 1  2  3  4 
22 18 12 11 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
16 25 22 
 1  2  3 
16 25 22 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
34 36 31 
 1  2  3 
34 36 31 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
21 40 40 
 1  2  3 
21 40 40 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "STOPPEDSMOKINGYEAR"                    
[19] "TOBACCOSMOKINGHISTORYINDICATOR"        
[20] "YEAROFTOBACCOSMOKINGONSET"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 101 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3466 
           1           27           NA            7           49          293 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          922          763         1357 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         336          223          109          125          179          135 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536           21          329           92           14           33 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
          19          196           36         2638          585          269 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        1938          697         1313         1454          658         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
         792          921          792          771          403          329 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
         232           29          364          240           84         3759 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
          NA         2948         2839           NA         1864         1532 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
        1516          799          612           NA          232          213 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         217          115          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          418          114          445           92 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        2428         2459         1556         1856         1669          471 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
         178          160          208          977         1257           NA 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 
         928         1059          387          428         5558           NA 
TCGA-GL-7966 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-J7-6720 
         112           NA           NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=84,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'STOPPEDSMOKINGYEAR':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[7] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
51  7 23  9 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 101 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
56 13 31  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   56    13    32 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
56 13 31  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   56    13    32 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
20 11  4 
[1] "table(vv)"
vv
N0 N1 N2 
20 11  4 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 
20 11  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
20 11  4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE',vnm)"
vv
  I  II III  IV 
 51   7  23   9 
[1] "table(vv)"
vv
  I  II III  IV 
 51   7  23   9 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 51   7  23   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 51   7  23   9 

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 6 1
  subtype2 8 1
subtype1 subtype2 
       7        9 
subtype1 subtype2 
       1        1 
$subtype1
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3473 TCGA-B3-3925 TCGA-B3-4103 TCGA-B9-4114 
        9.63        53.79        25.08         3.58         5.88         0.69 
TCGA-B9-4117 
        0.46 

$subtype2
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 
       58.45        13.55        30.31         4.11         4.44        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       10.82         3.02         1.08 

subtype1 subtype2 
    0.46     1.08 
subtype1 subtype2 
   53.79    58.45 
subtype1 subtype2 
    5.88    10.82 
[1] "0.5 - 53.8 (5.9)"  "1.1 - 58.5 (10.8)"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
[1] "hr=" "1.8"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 3 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    3    6
        clus
vv       subtype1 subtype2
  FEMALE        1        3
  MALE          6        6
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       1 
character(0)
D1V5, multiclass
D1V6, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       2 
character(0)
D1V7, multiclass
    clus
vv   subtype1 subtype2
  M0        4        5
  M1        1        0
D1V8, multiclass

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 1
  subtype2 6 1
  subtype3 5 0
subtype1 subtype2 subtype3 
       4        7        5 
subtype1 subtype2 subtype3 
       1        1        0 
$subtype1
TCGA-AL-3467 TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4115 
       58.45        30.31        50.50        10.82 

$subtype2
TCGA-AL-3466 TCGA-AL-3473 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4116 
        9.63        25.08         3.58         5.88         4.44         3.02 
TCGA-B9-4117 
        0.46 

$subtype3
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-4617 
       53.79        13.55         4.11         0.69         1.08 

subtype1 subtype2 subtype3 
   10.82     0.46     0.69 
subtype1 subtype2 subtype3 
   58.45    25.08    53.79 
subtype1 subtype2 subtype3 
  40.405    4.440    4.110 
[1] "10.8 - 58.5 (40.4)" "0.5 - 25.1 (4.4)"   "0.7 - 53.8 (4.1)"  
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 1 3
  subtype2 2 5
  subtype3 1 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    2    5
  subtype3    1    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        2        1
  MALE          3        5        4
D2V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)
D2V5, multiclass
D2V6, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       2 
character(0)
D2V7, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        5        3 
[1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[8] "subtype2"
    clus
vv   subtype2 subtype3
  M0        4        3
  M1        1        0
D2V8, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        5        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 21  3
  subtype2 43  7
  subtype3 16  4
subtype1 subtype2 subtype3 
      24       50       20 
subtype1 subtype2 subtype3 
       3        7        4 
$subtype1
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7732 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 
        0.03         0.69         0.03        53.79        13.55        44.61 
TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
        7.33         5.88        50.50         1.08         6.44         1.18 
TCGA-BQ-5880 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7840 
       43.17         2.76        96.92         3.78        13.61         3.75 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-G7-6790 TCGA-G7-6795 TCGA-GL-6846 TCGA-GL-7966 
       80.84        51.16        32.12        30.51       182.73         3.68 

$subtype2
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3467 
       15.95        35.18         0.89         0.23         1.61        58.45 
TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4104 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-5155 
       30.31         3.58         4.44         0.69        10.82         0.62 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       86.73        63.72        22.92        47.80        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 
       26.04        25.35        10.82         7.63         7.89       123.58 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       14.63         3.02        61.02        54.87        15.48         5.26 
TCGA-G7-6792 TCGA-G7-6797 
       41.33        12.72 

$subtype3
TCGA-A4-7583 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4116 
        0.10         9.63        25.08        11.05         4.11         3.02 
TCGA-B9-4117 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5888 
        0.46        19.23         8.84        21.63        30.28        13.25 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DZ-6131 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6793 
        0.95        11.97        79.82         5.85         6.84        11.05 
TCGA-G7-6796 TCGA-G7-7502 
       34.82        14.07 

subtype1 subtype2 subtype3 
    0.03     0.23     0.10 
subtype1 subtype2 subtype3 
  182.73   129.86    79.82 
subtype1 subtype2 subtype3 
   10.44    23.69    11.05 
[1] "0.0 - 182.7 (10.4)" "0.2 - 129.9 (23.7)" "0.1 - 79.8 (11.1)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[91] "subtype2" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[91] "subtype2" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[19] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[31] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[37] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[73] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[91] "subtype2" "subtype3" "subtype1" "subtype1"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  6 21
  subtype2 19 35
  subtype3  7 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   21
  subtype2   19   35
  subtype3    7   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       19        7
  MALE         21       35       13
D3V4, continuous
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 15  4
  subtype2 19  6
  subtype3 32  2
subtype1 subtype2 subtype3 
      19       25       34 
subtype1 subtype2 subtype3 
       4        6        2 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-AL-7173 TCGA-B1-5398 TCGA-BQ-5880 TCGA-BQ-5883 
        0.03        35.18        44.61        11.05        43.17        40.83 
TCGA-BQ-5884 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7059 
       26.04        13.25        10.82        44.84        26.27         7.63 
TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 
        3.78        24.46        14.63        80.84        61.02         5.26 
TCGA-G7-6796 
       34.82 

$subtype2
TCGA-A4-7287 TCGA-A4-7915 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.69         0.23        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       22.92        21.63        26.04        25.35         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7056 
       11.97         7.89         2.76       123.58        93.34        20.12 
TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-6846 
       11.28         7.13        79.82         6.84        11.05       182.73 
TCGA-GL-7966 
        3.68 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-B1-7332 
       15.95         0.10         0.03         0.89         1.61         7.33 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-5885 TCGA-BQ-7045 
        0.62         6.44         1.18        47.80        30.28        48.26 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-DW-5560 
       96.92        61.28        50.37        49.84         7.00        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.74         3.75 
TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6790 
        3.02        51.16        54.87        15.48         5.85        32.12 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
       41.33        30.51        12.72        14.07 

subtype1 subtype2 subtype3 
    0.03     0.23     0.03 
subtype1 subtype2 subtype3 
   80.84   182.73   129.86 
subtype1 subtype2 subtype3 
  26.040   11.970   14.775 
[1] "0.0 - 80.8 (26.0)"  "0.2 - 182.7 (12.0)" "0.0 - 129.9 (14.8)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[67] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[67] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype1"
[25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[43] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[67] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[73] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  6 15
  subtype2 12 14
  subtype3 10 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   15
  subtype2   12   14
  subtype3   10   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       12       10
  MALE         15       14       28
D4V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       6        1       13 
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[19] "subtype3"
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 15  7
  subtype2 16  2
  subtype3 10  2
  subtype4  9  2
subtype1 subtype2 subtype3 subtype4 
      22       18       12       11 
subtype1 subtype2 subtype3 subtype4 
       7        2        2        2 
$subtype1
TCGA-AL-3466 TCGA-AL-3467 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
        9.63        58.45         4.44        19.23         8.84        22.92 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       21.63        40.83        26.04        25.35        13.25        10.82 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 
        0.95         7.89         2.76        93.34        49.84        20.12 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-6793 
        7.13        79.82         6.84        11.05 

$subtype2
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4113 
       53.79        13.55        30.31         3.58         4.11        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5878 
        0.69        10.82         3.02         0.46         1.08        63.72 
TCGA-BQ-5885 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6795 
       30.28        11.61        13.61        51.16         5.85        30.51 

$subtype3
TCGA-AL-3473 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5892 
       25.08        43.17        47.80        26.04         7.63        11.97 
TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-G7-6790 
      123.58        61.28        50.37        11.28         7.00        32.12 

$subtype4
TCGA-B3-4103 TCGA-B9-5156 TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7059 TCGA-BQ-7062 
        5.88         6.44        48.26        44.84         7.63         3.78 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.84        61.02        54.87        15.48         5.26 

subtype1 subtype2 subtype3 subtype4 
    0.95     0.46     7.00     3.78 
subtype1 subtype2 subtype3 subtype4 
   93.34    63.72   123.58    80.84 
subtype1 subtype2 subtype3 subtype4 
   16.24    12.58    29.08    15.48 
[1] "0.9 - 93.3 (16.2)"  "0.5 - 63.7 (12.6)"  "7.0 - 123.6 (29.1)"
[4] "3.8 - 80.8 (15.5)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 11 11
  subtype2  6 12
  subtype3  1 11
  subtype4  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   11
  subtype2    6   12
  subtype3    1   11
  subtype4    2    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       11        6        1        2
  MALE         11       12       11        9
D5V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        3        1        2 
[1] "subtype2" "subtype2" "subtype2"
D5V5, multiclass
D5V6, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      15        3        7        1 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype2"
D5V7, multiclass
D5V8, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 10  6
  subtype2 22  3
  subtype3 18  4
subtype1 subtype2 subtype3 
      16       25       22 
subtype1 subtype2 subtype3 
       6        3        4 
$subtype1
TCGA-AL-3467 TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 
       58.45         4.44         3.02         8.84        22.92        40.83 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-DZ-6132 
       13.25        10.82         7.89         2.76        44.84        80.84 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6793 
       15.48         5.26         6.84        11.05 

$subtype2
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 
        9.63        53.79        13.55        30.31         3.58         4.11 
TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
        5.88        50.50         0.69        10.82         0.46         1.08 
TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7051 TCGA-BQ-7062 
       63.72        30.28         0.95       123.58        50.37         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6790 
       11.61        13.61        51.16        54.87         5.85        32.12 
TCGA-G7-6795 
       30.51 

$subtype3
TCGA-AL-3473 TCGA-B9-5156 TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       25.08         6.44        19.23        43.17        47.80        21.63 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-7045 
       26.04        26.04        25.35         7.63        11.97        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        49.84        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6134 
        7.00         7.13        79.82        61.02 

subtype1 subtype2 subtype3 
    2.76     0.46     6.44 
subtype1 subtype2 subtype3 
   80.84   123.58    93.34 
subtype1 subtype2 subtype3 
  10.935   13.550   25.215 
[1] "2.8 - 80.8 (10.9)"  "0.5 - 123.6 (13.6)" "6.4 - 93.3 (25.2)" 
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2  6 19
  subtype3  5 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2    6   19
  subtype3    5   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        6        5
  MALE          7       19       17
D6V4, continuous
D6V5, multiclass
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 29  4
  subtype2 27  7
  subtype3 24  3
subtype1 subtype2 subtype3 
      33       34       27 
subtype1 subtype2 subtype3 
       4        7        3 
$subtype1
TCGA-A4-7286 TCGA-A4-7585 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
        0.03        35.18        25.08        11.05         7.33         3.58 
TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        6.44        86.73        63.72        43.17        47.80        21.63 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 
       26.04        26.04         7.63         0.95        11.97        96.92 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 
       61.28        50.37        11.28         7.63         7.13         3.78 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6131 TCGA-DZ-6135 
       13.61        37.55         3.75        14.63        79.82        54.87 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 
       32.12        41.33        34.82 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3466 TCGA-AL-3472 TCGA-AL-7173 
        0.69         0.89         0.23         9.63        30.31        44.61 
TCGA-B3-4103 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 
        5.88         4.44        19.23         8.84        22.92        40.83 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
       25.35        10.82         2.76        48.26        93.34        44.84 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
       49.84        20.12         7.00        11.61       129.86        35.93 
TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 
       24.46        80.84        61.02        15.48         5.26         6.84 
TCGA-G7-6793 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       11.05        14.07       182.73         3.68 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-AL-3467 TCGA-AL-3468 
       15.95         0.10         0.03         1.61        58.45        53.79 
TCGA-AL-3471 TCGA-B3-3926 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       13.55         4.11        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5885 TCGA-BQ-5888 
        0.46         1.08         0.62         1.18        30.28        13.25 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6133 
        7.89       123.58        26.27        13.74         3.02        51.16 
TCGA-EV-5902 TCGA-G7-6795 TCGA-G7-6797 
        5.85        30.51        12.72 

subtype1 subtype2 subtype3 
    0.03     0.23     0.03 
subtype1 subtype2 subtype3 
   96.92   182.73   123.58 
subtype1 subtype2 subtype3 
  25.080   17.355   10.820 
[1] "0.0 - 96.9 (25.1)"  "0.2 - 182.7 (17.4)" "0.0 - 123.6 (10.8)"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[49] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[91] "subtype3" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[49] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[91] "subtype3" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[43] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[49] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[55] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[61] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[79] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[85] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[91] "subtype3" "subtype2" "subtype2" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  7 27
  subtype2 15 21
  subtype3 10 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   27
  subtype2   15   21
  subtype3   10   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       15       10
  MALE         27       21       21
D7V4, continuous
D7V5, multiclass
D7V6, multiclass
D7V7, multiclass
D7V8, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 17  2
  subtype2 29  7
  subtype3 34  5
subtype1 subtype2 subtype3 
      19       36       39 
subtype1 subtype2 subtype3 
       2        7        5 
$subtype1
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-AL-3467 TCGA-AL-3468 
       15.95         0.10         0.03         1.61        58.45        53.79 
TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 
       13.55         4.11         5.88        50.50         0.69         3.02 
TCGA-B9-4617 TCGA-B9-7268 TCGA-BQ-7044 TCGA-DW-7839 TCGA-DZ-6133 TCGA-EV-5902 
        1.08         1.18       123.58        13.74        51.16         5.85 
TCGA-G7-6797 
       12.72 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-4104 
        0.69         0.89         0.23        30.31        44.61         4.44 
TCGA-B9-5155 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 
        0.62         8.84        22.92        40.83        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
       10.82         7.89         2.76        48.26        93.34        44.84 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
       49.84        26.27        20.12        11.61       129.86        35.93 
TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
       24.46         3.02        80.84        61.02        15.48         5.26 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
        6.84        11.05        34.82        14.07       182.73         3.68 

$subtype3
TCGA-A4-7286 TCGA-A4-7585 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 
        0.03        35.18         9.63        25.08        11.05         7.33 
TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        3.58        10.82         0.46         6.44        86.73        19.23 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.17        47.80        21.63        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7050 
       26.04         7.63         0.95        11.97        96.92        61.28 
TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.37        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6131 TCGA-DZ-6135 
       13.61        37.55         3.75        14.63        79.82        54.87 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       32.12        41.33        30.51 

subtype1 subtype2 subtype3 
    0.03     0.23     0.03 
subtype1 subtype2 subtype3 
  123.58   182.73    96.92 
subtype1 subtype2 subtype3 
    5.88    17.80    19.23 
[1] "0.0 - 123.6 (5.9)"  "0.2 - 182.7 (17.8)" "0.0 - 96.9 (19.2)" 
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[85] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[91] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[85] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[91] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[49] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[73] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[79] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[85] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[91] "subtype1" "subtype2" "subtype2" "subtype2"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  7 14
  subtype2 17 23
  subtype3  8 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   14
  subtype2   17   23
  subtype3    8   32
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       17        8
  MALE         14       23       32
D8V4, continuous
D8V5, multiclass
D8V6, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       17       16 
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype2" "subtype2"
D8V7, multiclass
D8V8, multiclass
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
                "PATHOLOGY.T"                 "PATHOLOGY.N" 
                           V7                            V8 
        "PATHOLOGICSPREAD(M)"                 "TUMOR.STAGE" 
> q(save="no")
