
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/CESC-TP/2403779/1.GDAC_mergedClustering.Finished/CESC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2330179/1.GDAC_clinicalDataPicker.Finished/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=32, in cluster file=122, common to both=32
[1]  6 32
[1] "CN_CNMF"
[1] 3
 1  2  3 
11  3 12 
 1  2  3 
11  3 12 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
 6  4 12  8  2 
 1  2  3  4 
 6  4 12  8 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
16  5  7 
 1  2  3 
16  5  7 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 4  5 19 
 1  2  3 
 4  5 19 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
11 14  7 
 1  2  3 
11 14  7 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 3 18 11 
 1  2  3 
 3 18 11 
[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] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 32 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1505          925         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
        2127         2892           NA           NA           NA          376 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        3096          183            8           53           40           25 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
          19           81           NA          178          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-HG-A2PA TCGA-HM-A3JK 
         773          168 
Variable 1:'AGE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=26,	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=10,	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=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'STOPPEDSMOKINGYEAR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "STOPPEDSMOKINGYEAR"                    
[5] "TOBACCOSMOKINGHISTORYINDICATOR"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 32 columns, 1 survival variables, and 5 non-survival variables.
AGE, nv=24, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=5, binary=FALSE, numeric=TRUE
STOPPEDSMOKINGYEAR, nv=4, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 10  0
  subtype2  3  0
  subtype3 11  1
subtype1 subtype2 subtype3 
      10        3       12 
subtype1 subtype2 subtype3 
       0        0        1 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
       49.48        30.41         2.66         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-FU-A23L 
        1.32         0.82         5.85         1.22 

$subtype2
TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-FU-A3NI 
       70.85        69.93         1.45 

$subtype3
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23K 
       42.38        36.76        95.08         0.62         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.99         2.17         0.07         1.02        25.41         5.52 

subtype1 subtype2 subtype3 
    0.26     1.45     0.07 
subtype1 subtype2 subtype3 
   49.48    70.85    95.08 
subtype1 subtype2 subtype3 
   2.200   69.930    3.845 
[1] "0.3 - 49.5 (2.2)"  "1.4 - 70.8 (69.9)" "0.1 - 95.1 (3.8)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[25] "subtype3"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  2  9
  subtype2  0  3
  subtype3  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    9
  subtype2    0    3
  subtype3    2   10
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        2
  YES        9        3       10
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype3 
       2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
D1V5, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       2        2 
character(0)
D1V6, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  6  0
  subtype2  4  0
  subtype3 10  1
  subtype4  5  3
subtype1 subtype2 subtype3 subtype4 
       6        4       11        8 
subtype1 subtype2 subtype3 subtype4 
       0        0        1        3 
$subtype1
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A1OD TCGA-EA-A3HU TCGA-EX-A3L1 
       49.48        70.85        42.38       101.79         2.66         6.94 

$subtype2
TCGA-BI-A0VS TCGA-DS-A0VN TCGA-DS-A1OC TCGA-FU-A3HZ 
       30.41        95.08        12.36         1.02 

$subtype3
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       36.76         2.66         6.02         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        5.85         1.22         1.45        25.41         5.52 

$subtype4
TCGA-DS-A0VM TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-EA-A1QT TCGA-EA-A3HQ 
       69.93         8.75        28.90        28.27         0.26         1.74 
TCGA-FU-A2QG TCGA-FU-A3HY 
        0.99         0.07 

subtype1 subtype2 subtype3 subtype4 
    2.66     1.02     0.62     0.07 
subtype1 subtype2 subtype3 subtype4 
  101.79    95.08    36.76    69.93 
subtype1 subtype2 subtype3 subtype4 
  45.930   21.385    2.660    5.245 
[1] "2.7 - 101.8 (45.9)" "1.0 - 95.1 (21.4)"  "0.6 - 36.8 (2.7)"  
[4] "0.1 - 69.9 (5.2)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[13] "subtype1" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[25] "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[13] "subtype1" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[25] "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[13] "subtype1" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[25] "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 1 5
  subtype2 2 2
  subtype3 3 9
  subtype4 2 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype2    2    2
  subtype3    3    9
  subtype4    2    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        2        3        2
  YES        5        2        9        6
D2V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        1        2 
character(0)
D2V5, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype3 subtype4 
       1        2        1 
character(0)
D2V6, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 14  1
  subtype2  4  1
  subtype3  7  0
subtype1 subtype2 subtype3 
      15        5        7 
subtype1 subtype2 subtype3 
       1        1        0 
$subtype1
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A3LQ 
       49.48        70.85        42.38        36.76         2.66         6.02 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU 
        0.26         1.74         1.32         0.82         0.62         2.66 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI 
        0.99         0.07         1.45 

$subtype2
TCGA-BI-A0VS TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC 
       30.41        69.93        95.08        28.27        12.36 

$subtype3
TCGA-DS-A1OD TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ 
      101.79         5.85         1.22         1.22         2.17         1.02 
TCGA-HG-A2PA 
       25.41 

subtype1 subtype2 subtype3 
    0.07    12.36     1.02 
subtype1 subtype2 subtype3 
   70.85    95.08   101.79 
subtype1 subtype2 subtype3 
    1.74    30.41     2.17 
[1] "0.1 - 70.8 (1.7)"   "12.4 - 95.1 (30.4)" "1.0 - 101.8 (2.2)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype3" "subtype1" "subtype3"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  1 15
  subtype2  3  2
  subtype3  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   15
  subtype2    3    2
  subtype3    2    5
     clus
vv    subtype1 subtype2 subtype3
  NO         1        3        2
  YES       15        2        5
D3V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype3 
       4        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
D3V5, continuous
D3V6, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  4  0
  subtype2  4  1
  subtype3 17  1
subtype1 subtype2 subtype3 
       4        5       18 
subtype1 subtype2 subtype3 
       0        1        1 
$subtype1
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-FU-A2QG TCGA-FU-A3HY 
       69.93        95.08         0.99         0.07 

$subtype2
TCGA-DS-A0VK TCGA-DS-A1OD TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       36.76       101.79         1.22         1.22         2.17 

$subtype3
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A1OB 
       49.48        30.41        70.85        42.38         2.66        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-EA-A3HT TCGA-EA-A3HU TCGA-EX-A1H5 TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        0.62         2.66         5.85         1.02         1.45        25.41 

subtype1 subtype2 subtype3 
    0.07     1.22     0.26 
subtype1 subtype2 subtype3 
   95.08   101.79    70.85 
subtype1 subtype2 subtype3 
  35.460    2.170    4.255 
[1] "0.1 - 95.1 (35.5)" "1.2 - 101.8 (2.2)" "0.3 - 70.8 (4.3)" 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype3" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype3" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[25] "subtype3" "subtype3" "subtype3"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  1  3
  subtype2  1  4
  subtype3  4 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    1    4
  subtype3    4   15
     clus
vv    subtype1 subtype2 subtype3
  NO         1        1        4
  YES        3        4       15
D4V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        1        3 
[1] "subtype3" "subtype3" "subtype3"
D4V5, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        2 
character(0)
D4V6, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  9  2
  subtype2 11  2
  subtype3  7  0
subtype1 subtype2 subtype3 
      11       13        7 
subtype1 subtype2 subtype3 
       2        2        0 
$subtype1
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 
       49.48        70.85         2.66        69.93        95.08         8.75 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-EA-A1QT TCGA-EX-A3L1 TCGA-FU-A3HY 
       28.27        12.36         0.26         6.94         0.07 

$subtype2
TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1OA TCGA-DS-A1OD TCGA-EA-A3HQ 
       30.41        42.38        36.76        28.90       101.79         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HG-A2PA 
        1.32         0.82         0.62         2.17         1.45        25.41 
TCGA-HM-A3JK 
        5.52 

$subtype3
TCGA-DS-A3LQ TCGA-EA-A3HU TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        6.02         2.66         5.85         1.22         1.22         0.99 
TCGA-FU-A3HZ 
        1.02 

subtype1 subtype2 subtype3 
    0.07     0.62     0.99 
subtype1 subtype2 subtype3 
   95.08   101.79     6.02 
subtype1 subtype2 subtype3 
   12.36     5.52     1.22 
[1] "0.1 - 95.1 (12.4)" "0.6 - 101.8 (5.5)" "1.0 - 6.0 (1.2)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[25] "subtype3" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1  3  8
  subtype2  3 11
  subtype3  2  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    8
  subtype2    3   11
  subtype3    2    5
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        2
  YES        8       11        5
D5V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        2        2 
character(0)
D5V5, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        1        2 
character(0)
D5V6, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  0
  subtype2 14  4
  subtype3 10  0
subtype1 subtype2 subtype3 
       3       18       10 
subtype1 subtype2 subtype3 
       0        4        0 
$subtype1
TCGA-DS-A3LQ TCGA-FU-A23K TCGA-FU-A3EO 
        6.02         1.22         2.17 

$subtype2
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1O9 
       49.48        70.85        42.38        36.76         2.66         8.75 
TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       28.90        28.27       101.79         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.82         0.62         5.85         1.45        25.41         5.52 

$subtype3
TCGA-BI-A0VS TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OC TCGA-EA-A3HU TCGA-EX-A3L1 
       30.41        69.93        95.08        12.36         2.66         6.94 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         0.99         0.07         1.02 

subtype1 subtype2 subtype3 
    1.22     0.26     0.07 
subtype1 subtype2 subtype3 
    6.02   101.79    95.08 
subtype1 subtype2 subtype3 
    2.17     7.30     4.80 
[1] "1.2 - 6.0 (2.2)"   "0.3 - 101.8 (7.3)" "0.1 - 95.1 (4.8)" 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  1  2
  subtype2  5 13
  subtype3  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    5   13
  subtype3    2    9
     clus
vv    subtype1 subtype2 subtype3
  NO         1        5        2
  YES        2       13        9
D6V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        3        2 
[1] "subtype2" "subtype2" "subtype2"
D6V5, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        2        1 
character(0)
D6V6, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
                    "STOPPEDSMOKINGYEAR" 
                                      V6 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
> q(save="no")
