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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/6185325/UCS-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/6154832/UCS-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=UCS-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oT=UCS-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/6154832/UCS-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/6185325/UCS-TP.mergedcluster.txt"

nPatients in clinical file=33, in cluster file=57, common to both=33
[1]  8 33
[1] "CN_CNMF"
[1] 3
 1  2  3 
13 12  7 
 1  2  3 
13 12  7 
[1] "METHLYATION_CNMF"
[1] 3
1 2 3 4 5 
7 8 6 4 8 
1 2 3 4 5 
7 8 6 4 8 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
11  8 13 
 1  2  3 
11  8 13 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 2  3 10  8  9 
 2  3  4  5 
 3 10  8  9 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
 9 14  2  8 
 1  2  4 
 9 14  8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 1 15 17 
 2  3 
15 17 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
10 15  2  6 
 1  2  4 
10 15  6 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
 1 16 16 
 2  3 
16 16 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "GLEASON_SCORE"                         
[14] "PSA_VALUE"                             
[15] "DAYS_TO_PSA"                           
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 33 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM 
          NA           NA           NA         1439           NA           NA 
TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
         730           NA           NA         2118           NA         1816 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
          NA           NA           NA           NA          497          424 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-NA-A4QW TCGA-NA-A4QX 
         438          219          145          295         2261          833 
TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC 
          NA           NA         2596           NA           NA          461 
TCGA-ND-A4WF TCGA-NG-A4VW TCGA-QM-A5NM 
          NA           NA          165 
Variable 1:'AGE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 33 columns, 1 survival variables, and 1 non-survival variables.
AGE, nv=21, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 4 9
  subtype2 5 7
  subtype3 4 3
subtype1 subtype2 subtype3 
      13       12        7 
subtype1 subtype2 subtype3 
       9        7        3 
$subtype1
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT 
       52.27        18.08        24.00        22.52        29.95        69.63 
TCGA-N5-A59E TCGA-N8-A4PN TCGA-N8-A56S TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R1 
       14.70        13.94         9.70        74.33        27.39         6.64 
TCGA-ND-A4WA 
       23.47 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RV TCGA-N5-A59F TCGA-N8-A4PI 
        4.64        47.31         4.87        59.70        11.87        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PP TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NG-A4VW 
       13.71        16.34         7.20        10.42        15.16        31.17 

$subtype3
TCGA-N5-A4RU TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4WF 
       50.17        14.40         4.77         3.72        85.35         5.49 
TCGA-QM-A5NM 
        5.42 

subtype1 subtype2 subtype3 
    6.64     4.64     3.72 
subtype1 subtype2 subtype3 
   74.33    59.70    85.35 
subtype1 subtype2 subtype3 
  23.470   14.435    5.490 
[1] "6.6 - 74.3 (23.5)" "4.6 - 59.7 (14.4)" "3.7 - 85.3 (5.5)" 
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[31] "subtype2" "subtype3"
D1V2, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 4
  subtype2 2 6
  subtype3 3 3
  subtype4 3 1
  subtype5 2 6
subtype1 subtype2 subtype3 subtype4 subtype5 
       7        8        6        4        8 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        6        3        1        6 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-NA-A4QW 
      102.41        52.27        18.08        13.94         4.77        74.33 
TCGA-NA-A4QX 
       27.39 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
        4.64         4.87        22.52        69.63        50.17        59.70 
TCGA-N5-A59E TCGA-ND-A4WF 
       14.70         5.49 

$subtype3
TCGA-N5-A4RF TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PP TCGA-ND-A4WC TCGA-NG-A4VW 
       47.31        11.87        26.63         7.20        15.16        31.17 

$subtype4
TCGA-N5-A4RN TCGA-N8-A4PO TCGA-NA-A4R1 TCGA-QM-A5NM 
       24.00        14.40         6.64         5.42 

$subtype5
TCGA-N5-A4RS TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A56S TCGA-NA-A4QY TCGA-NA-A5I1 
       29.95        13.71        16.34         9.70         3.72        85.35 
TCGA-ND-A4W6 TCGA-ND-A4WA 
       10.42        23.47 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.77     4.64     7.20     5.42     3.72 
subtype1 subtype2 subtype3 subtype4 subtype5 
  102.41    69.63    47.31    24.00    85.35 
subtype1 subtype2 subtype3 subtype4 subtype5 
  27.390   18.610   20.895   10.520   15.025 
[1] "4.8 - 102.4 (27.4)" "4.6 - 69.6 (18.6)"  "7.2 - 47.3 (20.9)" 
[4] "5.4 - 24.0 (10.5)"  "3.7 - 85.3 (15.0)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype4" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
[19] "subtype4" "subtype3" "subtype1" "subtype5" "subtype1" "subtype1"
[25] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype3"
[31] "subtype2" "subtype3" "subtype4"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype4" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
[19] "subtype4" "subtype3" "subtype1" "subtype5" "subtype1" "subtype1"
[25] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype3"
[31] "subtype2" "subtype3" "subtype4"
 [1] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
 [7] "subtype4" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype3" "subtype3" "subtype5" "subtype5" "subtype1"
[19] "subtype4" "subtype3" "subtype1" "subtype5" "subtype1" "subtype1"
[25] "subtype5" "subtype4" "subtype5" "subtype5" "subtype5" "subtype3"
[31] "subtype2" "subtype3" "subtype4"
D2V2, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  4  7
  subtype2  6  2
  subtype3  3 10
subtype1 subtype2 subtype3 
      11        8       13 
subtype1 subtype2 subtype3 
       7        2       10 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N8-A4PN TCGA-N8-A4PP 
      102.41        52.27         4.64        22.52        13.94         7.20 
TCGA-N8-A4PQ TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4W6 TCGA-ND-A4WF 
        4.77        74.33        27.39        10.42         5.49 

$subtype2
TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-ND-A4WC 
       47.31        24.00        26.63        16.34        14.40        15.16 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.17         5.42 

$subtype3
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       18.08        29.95        69.63        50.17        59.70        14.70 
TCGA-N5-A59F TCGA-N8-A4PL TCGA-N8-A56S TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
       11.87        13.71         9.70         3.72         6.64        85.35 
TCGA-ND-A4WA 
       23.47 

subtype1 subtype2 subtype3 
    4.64     5.42     3.72 
subtype1 subtype2 subtype3 
  102.41    47.31    85.35 
subtype1 subtype2 subtype3 
   13.94    20.17    18.08 
[1] "4.6 - 102.4 (13.9)" "5.4 - 47.3 (20.2)"  "3.7 - 85.3 (18.1)" 
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype2"
 [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[31] "subtype2" "subtype2"
D3V2, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype2 2 1
  subtype3 3 7
  subtype4 1 7
  subtype5 6 3
subtype2 subtype3 subtype4 subtype5 
       3       10        8        9 
subtype2 subtype3 subtype4 subtype5 
       1        7        7        3 
$subtype2
TCGA-N5-A4RN TCGA-N5-A4RU TCGA-N5-A4RV 
       24.00        50.17        59.70 

$subtype3
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N8-A4PN TCGA-N8-A4PQ 
      102.41        52.27         4.64        22.52        13.94         4.77 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4W6 TCGA-ND-A4WF 
       74.33        27.39        10.42         5.49 

$subtype4
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A59E TCGA-N8-A4PL TCGA-N8-A56S TCGA-NA-A4QY 
       18.08        29.95        14.70        13.71         9.70         3.72 
TCGA-NA-A5I1 TCGA-ND-A4WA 
       85.35        23.47 

$subtype5
TCGA-N5-A4RF TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP 
       47.31        11.87        26.63        16.34        14.40         7.20 
TCGA-ND-A4WC TCGA-NG-A4VW TCGA-QM-A5NM 
       15.16        31.17         5.42 

subtype2 subtype3 subtype4 subtype5 
   24.00     4.64     3.72     5.42 
subtype2 subtype3 subtype4 subtype5 
   59.70   102.41    85.35    47.31 
subtype2 subtype3 subtype4 subtype5 
   50.17    18.23    16.39    15.16 
[1] "24.0 - 59.7 (50.2)" "4.6 - 102.4 (18.2)" "3.7 - 85.3 (16.4)" 
[4] "5.4 - 47.3 (15.2)" 
 [1] "subtype3" "subtype3" "subtype3" "subtype5" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype5"
[13] "subtype5" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
[19] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[25] "subtype3" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
 [1] "subtype3" "subtype3" "subtype3" "subtype5" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype5"
[13] "subtype5" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
[19] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[25] "subtype3" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
 [1] "subtype3" "subtype3" "subtype3" "subtype5" "subtype4" "subtype2"
 [7] "subtype3" "subtype4" "subtype2" "subtype2" "subtype4" "subtype5"
[13] "subtype5" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
[19] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[25] "subtype3" "subtype4" "subtype5" "subtype3" "subtype5" "subtype5"
D4V2, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 3 6
  subtype2 5 9
  subtype4 4 4
subtype1 subtype2 subtype4 
       9       14        8 
subtype1 subtype2 subtype4 
       6        9        4 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N8-A4PP TCGA-N8-A4PQ 
      102.41         4.64        47.31        18.08         7.20         4.77 
TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-ND-A4WF 
       27.39         6.64         5.49 

$subtype2
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV 
       52.27         4.87        24.00        22.52        50.17        59.70 
TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-NA-A4QW TCGA-NA-A5I1 
       11.87        26.63        13.71        13.94        74.33        85.35 
TCGA-ND-A4W6 TCGA-ND-A4WA 
       10.42        23.47 

$subtype4
TCGA-N5-A59E TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S TCGA-NA-A4QY TCGA-ND-A4WC 
       14.70        16.34        14.40         9.70         3.72        15.16 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.17         5.42 

subtype1 subtype2 subtype4 
    4.64     4.87     3.72 
subtype1 subtype2 subtype4 
  102.41    85.35    31.17 
subtype1 subtype2 subtype4 
   7.200   23.735   14.550 
[1] "4.6 - 102.4 (7.2)" "4.9 - 85.3 (23.7)" "3.7 - 31.2 (14.6)"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype2"
[13] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
D5V2, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype2  7  8
  subtype3  6 11
subtype2 subtype3 
      15       17 
subtype2 subtype3 
       8       11 
$subtype2
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A59E 
      102.41         4.64        47.31        18.08        69.63        14.70 
TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-NA-A4R1 TCGA-ND-A4WC 
       16.34         7.20         4.77         9.70         6.64        15.16 
TCGA-ND-A4WF TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        31.17         5.42 

$subtype3
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.27         4.87        24.00        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO 
       59.70        11.87        26.63        13.71        13.94        14.40 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       74.33        27.39        85.35        10.42        23.47 

subtype2 subtype3 
    4.64     4.87 
subtype2 subtype3 
  102.41    85.35 
subtype2 subtype3 
    14.7     24.0 
[1] "4.6 - 102.4 (14.7)" "4.9 - 85.3 (24.0)" 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[31] "subtype2" "subtype2"
[1] "hr=" "1.1"
D6V2, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  3  7
  subtype2  5 10
  subtype4  4  2
subtype1 subtype2 subtype4 
      10       15        6 
subtype1 subtype2 subtype4 
       7       10        2 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A59E TCGA-N8-A4PP 
      102.41         4.64        47.31        18.08        14.70         7.20 
TCGA-N8-A4PQ TCGA-NA-A4QX TCGA-NA-A4QY TCGA-ND-A4WF 
        4.77        27.39         3.72         5.49 

$subtype2
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.27         4.87        24.00        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-NA-A4QW 
       59.70        11.87        26.63        13.71        13.94        74.33 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       85.35        10.42        23.47 

$subtype4
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S TCGA-ND-A4WC TCGA-NG-A4VW TCGA-QM-A5NM 
       16.34        14.40         9.70        15.16        31.17         5.42 

subtype1 subtype2 subtype4 
    3.72     4.87     5.42 
subtype1 subtype2 subtype4 
  102.41    85.35    31.17 
subtype1 subtype2 subtype4 
   10.95    24.00    14.78 
[1] "3.7 - 102.4 (10.9)" "4.9 - 85.3 (24.0)"  "5.4 - 31.2 (14.8)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype4"
[19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype4"
[19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype4"
[19] "subtype1" "subtype1" "subtype4" "subtype2" "subtype1" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
[31] "subtype4"
D7V2, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype2  5 11
  subtype3  8  8
subtype2 subtype3 
      16       16 
subtype2 subtype3 
      11        8 
$subtype2
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.27         4.87        24.00        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PN TCGA-NA-A4QW 
       59.70        11.87        26.63        13.71        13.94        74.33 
TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       27.39        85.35        10.42        23.47 

$subtype3
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A59E 
      102.41         4.64        47.31        18.08        69.63        14.70 
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-NA-A4R1 
       16.34        14.40         7.20         4.77         9.70         6.64 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NG-A4VW TCGA-QM-A5NM 
       15.16         5.49        31.17         5.42 

subtype2 subtype3 
    4.87     4.64 
subtype2 subtype3 
   85.35   102.41 
subtype2 subtype3 
  25.315   14.550 
[1] "4.9 - 85.3 (25.3)"  "4.6 - 102.4 (14.6)"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[25] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3"
[1] "hr=" "1"  
D8V2, continuous
> q(save="no")
