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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/CESC-TP/3586858/CESC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/CESC-TP/3349247/CESC-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=50, in cluster file=134, common to both=48
[1]  8 48
[1] "CN_CNMF"
[1] 3
 1  2  3 
18  7 17 
 1  2  3 
18  7 17 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
25 16  7 
 1  2  3 
25 16  7 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
26 10  7 
 1  2  3 
26 10  7 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 6 31  6 
 1  2  3 
 6 31  6 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
22 15  3  8 
 1  2  3  4 
22 15  3  8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2 
39  9 
 1  2 
39  9 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
22 18  8 
 1  2  3 
22 18  8 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
 5 18 25 
 1  2  3 
 5 18 25 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 48 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
        1505          925         1112         5385           NA           NA 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
        1616           NA           NA           NA         2382         2155 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
        1289           NA           81         2127         2892           NA 
TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT 
          NA           NA          376         3096          183            8 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A439 
          53           40           25           19           81           20 
TCGA-EA-A43B TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K 
          54           NA          178          241          211           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
          37           30           66            2           31           44 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
          48           24          106          773           NA          168 
Variable 1:'AGE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "NUMBER.OF.LYMPH.NODES"                 
[7] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B   T4 
   6   17    5    2    3    3    6    1    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 48 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=32, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 15  2
  subtype2  3  4
  subtype3 16  1
subtype1 subtype2 subtype3 
      17        7       17 
subtype1 subtype2 subtype3 
       2        4        1 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A2LY TCGA-DS-A0VK 
       49.48        30.41        67.46        53.13        78.31        36.76 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A439 TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A3JK 
        0.66         5.85         1.22         1.45         5.52 

$subtype2
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-EA-A43B 
        5.46        35.61        40.93        70.85        69.93         1.78 
TCGA-HM-A3JJ 
       21.67 

$subtype3
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-EA-A3HT 
       36.56       177.04         2.43        42.38        95.08         0.62 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        7.92         6.94         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.58         0.79         3.48        25.41 

subtype1 subtype2 subtype3 
    0.26     1.78     0.07 
subtype1 subtype2 subtype3 
   78.31    70.85   177.04 
subtype1 subtype2 subtype3 
    5.52    35.61     2.43 
[1] "0.3 - 78.3 (5.5)"  "1.8 - 70.8 (35.6)" "0.1 - 177.0 (2.4)"
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[13] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  5 13
  subtype2  4  3
  subtype3  4 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   13
  subtype2    4    3
  subtype3    4   13
     clus
vv    subtype1 subtype2 subtype3
  NO         5        4        4
  YES       13        3       13
D1V4, continuous
D1V5, binary
          cls
clus        0  1
  subtype1 12  5
  subtype2  4  1
  subtype3  7  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    5
  subtype2    4    1
  subtype3    7    8
    clus
vv   subtype1 subtype2 subtype3
  M0       12        4        7
  MX        5        1        8
D1V6, binary
          cls
clus        0  1
  subtype1 11  6
  subtype2  2  3
  subtype3 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    6
  subtype2    2    3
  subtype3   11    5
    clus
vv   subtype1 subtype2 subtype3
  N0       11        2       11
  N1        6        3        5
D1V7, continuous
D1V8, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 17  7
  subtype2 14  2
  subtype3  6  1
subtype1 subtype2 subtype3 
      24       16        7 
subtype1 subtype2 subtype3 
       7        2        1 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MN TCGA-DS-A0VK 
       49.48       177.04         5.46        67.46        40.93        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB 
        2.66        69.93        95.08         8.75        28.90        28.27 
TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       12.36         6.02         0.26         1.74         1.32         0.82 
TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        5.85         0.99         0.07         1.45         1.58         0.79 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       30.41        36.56         2.43        78.31        70.85        42.38 
TCGA-DS-A1OD TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A43B TCGA-EX-A3L1 TCGA-FU-A23L 
      101.79         0.62         2.66         1.78         6.94         1.22 
TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.48        25.41        21.67         5.52 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A3EO 
       53.13        35.61         0.66         7.92         1.22         2.17 
TCGA-FU-A3HZ 
        1.02 

subtype1 subtype2 subtype3 
    0.07     0.62     0.66 
subtype1 subtype2 subtype3 
  177.04   101.79    53.13 
subtype1 subtype2 subtype3 
   5.935   14.305    2.170 
[1] "0.1 - 177.0 (5.9)"  "0.6 - 101.8 (14.3)" "0.7 - 53.1 (2.2)"  
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype3" "subtype2" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  7 18
  subtype2  7  9
  subtype3  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   18
  subtype2    7    9
  subtype3    2    5
     clus
vv    subtype1 subtype2 subtype3
  NO         7        7        2
  YES       18        9        5
D2V4, continuous
D2V5, binary
          cls
clus        0  1
  subtype1 15  6
  subtype2 11  4
  subtype3  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    6
  subtype2   11    4
  subtype3    3    4
    clus
vv   subtype1 subtype2 subtype3
  M0       15       11        3
  MX        6        4        4
D2V6, binary
          cls
clus        0  1
  subtype1 11 11
  subtype2 11  4
  subtype3  5  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   11
  subtype2   11    4
  subtype3    5    2
    clus
vv   subtype1 subtype2 subtype3
  N0       11       11        5
  N1       11        4        2
D2V7, continuous
D2V8, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 22  4
  subtype2  6  3
  subtype3  6  1
subtype1 subtype2 subtype3 
      26        9        7 
subtype1 subtype2 subtype3 
       4        3        1 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-DR-A0ZL 
       49.48        36.56       177.04        67.46         2.43        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
       42.38        36.76         2.66        95.08         6.02         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A1H5 
        1.74         1.32         0.82         0.62         2.66         5.85 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        1.22         0.99         0.07         1.45         1.58         0.79 
TCGA-FU-A3YQ TCGA-HM-A3JJ 
        3.48        21.67 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VM TCGA-DS-A1OB 
       30.41         5.46        40.93        78.31        69.93        28.27 
TCGA-DS-A1OC TCGA-DS-A1OD TCGA-FU-A3HZ 
       12.36       101.79         1.02 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A3EO 
       53.13        35.61         0.66         7.92         1.22         2.17 
TCGA-HG-A2PA 
       25.41 

subtype1 subtype2 subtype3 
    0.07     1.02     0.66 
subtype1 subtype2 subtype3 
  177.04   101.79    53.13 
subtype1 subtype2 subtype3 
    2.66    30.41     7.92 
[1] "0.1 - 177.0 (2.7)"  "1.0 - 101.8 (30.4)" "0.7 - 53.1 (7.9)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[31] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  7 19
  subtype2  5  5
  subtype3  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   19
  subtype2    5    5
  subtype3    2    5
     clus
vv    subtype1 subtype2 subtype3
  NO         7        5        2
  YES       19        5        5
D3V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       9        2        3 
 [1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
D3V5, binary
          cls
clus        0  1
  subtype1 15  9
  subtype2  7  0
  subtype3  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    9
  subtype2    7    0
  subtype3    3    4
    clus
vv   subtype1 subtype2 subtype3
  M0       15        7        3
  MX        9        0        4
D3V6, binary
          cls
clus        0  1
  subtype1 15 10
  subtype2  4  3
  subtype3  5  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   10
  subtype2    4    3
  subtype3    5    2
    clus
vv   subtype1 subtype2 subtype3
  N0       15        4        5
  N1       10        3        2
D3V7, continuous
D3V8, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5  0
  subtype2 24  7
  subtype3  5  1
subtype1 subtype2 subtype3 
       5       31        6 
subtype1 subtype2 subtype3 
       0        7        1 
$subtype1
TCGA-BI-A0VS TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-FU-A3HZ 
       30.41        12.36       101.79         6.02         1.02 

$subtype2
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MK 
       49.48        36.56       177.04         5.46        67.46         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OB TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08        28.27         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG 
        0.82         0.62         2.66         5.85         1.22         0.99 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ 
       21.67 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A3EO 
       53.13        35.61         0.66         7.92         1.22         2.17 

subtype1 subtype2 subtype3 
    1.02     0.07     0.66 
subtype1 subtype2 subtype3 
  101.79   177.04    53.13 
subtype1 subtype2 subtype3 
  12.360    5.460    5.045 
[1] "1.0 - 101.8 (12.4)" "0.1 - 177.0 (5.5)"  "0.7 - 53.1 (5.0)"  
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  3  3
  subtype2  9 22
  subtype3  2  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    9   22
  subtype3    2    4
     clus
vv    subtype1 subtype2 subtype3
  NO         3        9        2
  YES        3       22        4
D4V4, continuous
D4V5, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 18  9
  subtype3  2  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   18    9
  subtype3    2    4
    clus
vv   subtype1 subtype2 subtype3
  M0        5       18        2
  MX        0        9        4
D4V6, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 17 11
  subtype3  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   17   11
  subtype3    4    2
    clus
vv   subtype1 subtype2 subtype3
  N0        3       17        4
  N1        2       11        2
D4V7, continuous
D4V8, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 16  5
  subtype2 12  3
  subtype3  2  1
  subtype4  7  1
subtype1 subtype2 subtype3 subtype4 
      21       15        3        8 
subtype1 subtype2 subtype3 subtype4 
       5        3        1        1 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-DR-A0ZM 
       49.48        30.41       177.04        67.46         2.43        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1OA TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        28.90       101.79         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB 
        1.32         0.82         5.85         1.22         1.45         0.79 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       25.41        21.67         5.52 

$subtype2
TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN 
       36.56         5.46        40.93        70.85        69.93        95.08 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A3HU TCGA-EA-A43B TCGA-EX-A3L1 
       28.27        12.36         6.02         2.66         1.78         6.94 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3TQ 
        0.99         0.07         1.58 

$subtype3
TCGA-DS-A1O9 TCGA-EA-A3HT TCGA-FU-A3YQ 
        8.75         0.62         3.48 

$subtype4
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A2LY TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23K 
       53.13        35.61        78.31         0.66         7.92         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ 
        2.17         1.02 

subtype1 subtype2 subtype3 subtype4 
    0.26     0.07     0.62     0.66 
subtype1 subtype2 subtype3 subtype4 
  177.04    95.08     8.75    78.31 
subtype1 subtype2 subtype3 subtype4 
   5.850    6.940    3.480    5.045 
[1] "0.3 - 177.0 (5.8)" "0.1 - 95.1 (6.9)"  "0.6 - 8.8 (3.5)"  
[4] "0.7 - 78.3 (5.0)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype4"
[31] "subtype2" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype4"
[31] "subtype2" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[19] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype4"
[31] "subtype2" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
[37] "subtype2" "subtype4" "subtype2" "subtype4" "subtype1" "subtype2"
[43] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  7 15
  subtype2  6  9
  subtype3  0  3
  subtype4  3  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   15
  subtype2    6    9
  subtype3    0    3
  subtype4    3    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         7        6        0        3
  YES       15        9        3        5
D5V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       4        6        1        3 
 [1] "subtype1" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
 [7] "subtype1" "subtype1" "subtype2" "subtype4" "subtype2" "subtype2"
[13] "subtype1"
D5V5, binary
          cls
clus        0  1
  subtype1 13  7
  subtype2 10  2
  subtype3  2  1
  subtype4  4  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    7
  subtype2   10    2
  subtype3    2    1
  subtype4    4    4
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       13       10        2        4
  MX        7        2        1        4
D5V6, binary
          cls
clus        0  1
  subtype1 12  8
  subtype2  6  7
  subtype3  3  0
  subtype4  6  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    8
  subtype2    6    7
  subtype3    3    0
  subtype4    6    2
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       12        6        3        6
  N1        8        7        0        2
D5V7, continuous
D5V8, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 30  8
  subtype2  7  2
subtype1 subtype2 
      38        9 
subtype1 subtype2 
       8        2 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OC 
        2.66        69.93        95.08         8.75        28.90        12.36 
TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
      101.79         0.26         1.74         1.32         0.82         0.62 
TCGA-EA-A3HU TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG 
        2.66         1.78         5.85         6.94         1.22         0.99 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

$subtype2
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DS-A1OB TCGA-DS-A3LQ TCGA-EA-A439 TCGA-EX-A1H6 
       53.13        35.61        28.27         6.02         0.66         7.92 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
        1.22         2.17         1.02 

subtype1 subtype2 
    0.07     0.66 
subtype1 subtype2 
  177.04    53.13 
subtype1 subtype2 
   6.395    6.020 
[1] "0.1 - 177.0 (6.4)" "0.7 - 53.1 (6.0)" 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[31] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[37] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[43] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[1] "hr=" "1.8"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 13 26
  subtype2  3  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   26
  subtype2    3    6
     clus
vv    subtype1 subtype2
  NO        13        3
  YES       26        6
D6V4, continuous
D6V5, binary
          cls
clus        0  1
  subtype1 24 10
  subtype2  5  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   10
  subtype2    5    4
    clus
vv   subtype1 subtype2
  M0       24        5
  MX       10        4
D6V6, binary
          cls
clus        0  1
  subtype1 22 13
  subtype2  5  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   13
  subtype2    5    4
    clus
vv   subtype1 subtype2
  N0       22        5
  N1       13        4
D6V7, continuous
D6V8, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 17  5
  subtype2 13  4
  subtype3  7  1
subtype1 subtype2 subtype3 
      22       17        8 
subtype1 subtype2 subtype3 
       5        4        1 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MK 
       49.48        30.41        36.56       177.04         5.46         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.93        78.31        70.85         2.66        69.93        95.08 
TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HU 
        8.75        28.27        12.36         6.02         0.26         2.66 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3TQ 
        6.94         1.22         0.07         1.58 

$subtype2
TCGA-C5-A1M5 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1OA TCGA-DS-A1OD TCGA-EA-A3HQ 
       67.46        42.38        36.76        28.90       101.79         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.32         0.82         0.62         5.85         1.02         1.45 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.79         3.48        25.41        21.67         5.52 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 TCGA-FU-A23K 
       53.13        35.61         0.66         1.78         7.92         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO 
        0.99         2.17 

subtype1 subtype2 subtype3 
    0.07     0.62     0.66 
subtype1 subtype2 subtype3 
  177.04   101.79    53.13 
subtype1 subtype2 subtype3 
  10.555    5.520    1.975 
[1] "0.1 - 177.0 (10.6)" "0.6 - 101.8 (5.5)"  "0.7 - 53.1 (2.0)"  
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[37] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1  8 14
  subtype2  6 12
  subtype3  2  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   14
  subtype2    6   12
  subtype3    2    6
     clus
vv    subtype1 subtype2 subtype3
  NO         8        6        2
  YES       14       12        6
D7V4, continuous
D7V5, binary
          cls
clus        0  1
  subtype1 15  4
  subtype2 11  6
  subtype3  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    4
  subtype2   11    6
  subtype3    3    4
    clus
vv   subtype1 subtype2 subtype3
  M0       15       11        3
  MX        4        6        4
D7V6, binary
          cls
clus        0  1
  subtype1 11  8
  subtype2 10  7
  subtype3  6  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    8
  subtype2   10    7
  subtype3    6    2
    clus
vv   subtype1 subtype2 subtype3
  N0       11       10        6
  N1        8        7        2
D7V7, continuous
D7V8, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  4  1
  subtype2 15  2
  subtype3 18  7
subtype1 subtype2 subtype3 
       5       17       25 
subtype1 subtype2 subtype3 
       1        2        7 
$subtype1
TCGA-C5-A1MI TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A3EO 
       35.61         0.66         7.92         1.22         2.17 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VM TCGA-DS-A0VN 
       30.41         5.46        40.93        78.31        69.93        95.08 
TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A3HU TCGA-EA-A43B TCGA-EX-A3L1 TCGA-FU-A23L 
       12.36         6.02         2.66         1.78         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
        0.99         0.07         1.02         1.58         0.79 

$subtype3
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        36.56       177.04        67.46        53.13         2.43 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1O9 TCGA-DS-A1OA 
       70.85        42.38        36.76         2.66         8.75        28.90 
TCGA-DS-A1OB TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       28.27       101.79         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.62         5.85         1.45         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

subtype1 subtype2 subtype3 
    0.66     0.07     0.26 
subtype1 subtype2 subtype3 
   35.61    95.08   177.04 
subtype1 subtype2 subtype3 
    2.17     5.46    21.67 
[1] "0.7 - 35.6 (2.2)"   "0.1 - 95.1 (5.5)"   "0.3 - 177.0 (21.7)"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  1  4
  subtype2  6 12
  subtype3  9 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    4
  subtype2    6   12
  subtype3    9   16
     clus
vv    subtype1 subtype2 subtype3
  NO         1        6        9
  YES        4       12       16
D8V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        6        6 
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
D8V5, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2 10  4
  subtype3 17  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2   10    4
  subtype3   17    7
    clus
vv   subtype1 subtype2 subtype3
  M0        2       10       17
  MX        3        4        7
D8V6, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 10  5
  subtype3 14 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   10    5
  subtype3   14   10
    clus
vv   subtype1 subtype2 subtype3
  N0        3       10       14
  N1        2        5       10
D8V7, continuous
D8V8, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
                    "DISTANT.METASTASIS" 
                                      V6 
                 "LYMPH.NODE.METASTASIS" 
                                      V7 
                 "NUMBER.OF.LYMPH.NODES" 
                                      V8 
                       "TUMOR.STAGECODE" 
> q(save="no")
