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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/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/ESCA-TP/6159635/ESCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/6154407/ESCA-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=ESCA-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=ESCA-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/ESCA-TP/6154407/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/6159635/ESCA-TP.mergedcluster.txt"

nPatients in clinical file=22, in cluster file=73, common to both=22
[1]  6 22
[1] "CN_CNMF"
[1] 3
 1  2  3 
 3 12  7 
 1  2  3 
 3 12  7 
[1] "METHLYATION_CNMF"
[1] 3
1 2 3 
8 6 8 
1 2 3 
8 6 8 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
 7  4 11 
 1  2  3 
 7  4 11 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 2  3 
11 11 
 2  3 
11 11 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
 4  2  6 10 
 1  3  4 
 4  6 10 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 2  3 
11 11 
 2  3 
11 11 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"          "VITALSTATUS"           "DAYSTODEATH"          
 [4] "DAYSTOLASTFOLLOWUP"    "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
 [7] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "DCCUPLOADDATE"        
[10] "GENDER"                "NUMBERPACKYEARSSMOKED" "GLEASON_SCORE"        
[13] "PSA_VALUE"             "DAYS_TO_PSA"           "BATCHNUMBER"          

Input Data has 15 rows and 22 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
          NA           NA           NA            1            8           16 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
          NA           NA           11          106          112          124 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
          NA          101           NA           NA          934          882 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
          NA           NA            4            2 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 22 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 4  7  9  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4     7    11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 4  7  9  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4     7    11 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
 8 10  3  1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
    8    10     4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
 8 10  3  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
    8    10     4 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype2 5 6
  subtype3 4 0
subtype1 subtype2 subtype3 
       3       11        4 
subtype1 subtype2 subtype3 
       0        6        0 
$subtype1
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 
        0.26         0.53         0.36 

$subtype2
TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.79         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.71        29.00         7.10         7.43 

$subtype3
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.03         4.08         0.13         0.07 

subtype1 subtype2 subtype3 
    0.26     0.79     0.03 
subtype1 subtype2 subtype3 
    0.53    30.71     4.08 
subtype1 subtype2 subtype3 
    0.36     3.68     0.10 
[1] "0.3 - 0.5 (0.4)"  "0.8 - 30.7 (3.7)" "0.0 - 4.1 (0.1)" 
 [1] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1        0        0         0         0          1          2
  subtype2        1        1         1         5          2          1
  subtype3        1        0         2         2          2          0
          vv
clus       STAGE IIIC
  subtype1          0
  subtype2          1
  subtype3          0
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  0  0     3
  subtype2  3  4     5
  subtype3  1  3     3
D1V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  0  1     2
  subtype2  4  6     2
  subtype3  4  3     0
D1V5, multiclass
D1V6, binary
          cls
clus        0  1
  subtype1  0  3
  subtype2  2 10
  subtype3  1  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    2   10
  subtype3    1    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        0        2        1
  MALE          3       10        6
D1V7, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        9        4 
 [1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype3"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 5 0
  subtype2 3 2
  subtype3 4 4
subtype1 subtype2 subtype3 
       5        5        8 
subtype1 subtype2 subtype3 
       0        2        4 
$subtype1
TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.53         0.36         4.08         0.13         0.07 

$subtype2
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         0.79         3.32         1.38        30.71 

$subtype3
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         3.48         3.68        18.35         3.16        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX 
        7.10         7.43 

subtype1 subtype2 subtype3 
    0.07     0.03     0.26 
subtype1 subtype2 subtype3 
    4.08    30.71    29.00 
subtype1 subtype2 subtype3 
    0.36     1.38     5.39 
[1] "0.1 - 4.1 (0.4)"  "0.0 - 30.7 (1.4)" "0.3 - 29.0 (5.4)"
 [1] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1        1        0         2         1          3          1
  subtype2        0        1         0         2          2          0
  subtype3        1        0         1         4          0          2
          vv
clus       STAGE IIIC
  subtype1          0
  subtype2          1
  subtype3          0
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  2     5
  subtype2  0  3     3
  subtype3  3  2     3
D2V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  4  3     1
  subtype2  2  3     1
  subtype3  2  4     2
D2V5, multiclass
D2V6, binary
          cls
clus       0 1
  subtype1 1 7
  subtype2 1 5
  subtype3 1 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2    1    5
  subtype3    1    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        1        1
  MALE          7        5        7
D2V7, continuous

Clustering(3) Variable = MIRSEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 5 1
  subtype2 1 0
  subtype3 6 5
subtype1 subtype2 subtype3 
       6        1       11 
subtype1 subtype2 subtype3 
       1        0        5 
$subtype1
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OM TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.03         0.53         0.79         4.08         0.13         0.07 

$subtype2
TCGA-IG-A625 
        0.36 

$subtype3
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.71        29.00         7.10         7.43 

subtype1 subtype2 subtype3 
    0.03     0.36     0.26 
subtype1 subtype2 subtype3 
    4.08     0.36    30.71 
subtype1 subtype2 subtype3 
    0.33     0.36     3.68 
[1] "0.0 - 4.1 (0.3)"  "0.4 - 0.4 (0.4)"  "0.3 - 30.7 (3.7)"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       6        1       11 
 [1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[1] "hr=" "3.8"
D3V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1        1        1         2         2          1          0
  subtype2        0        0         0         0          3          1
  subtype3        1        0         1         5          1          2
          vv
clus       STAGE IIIC
  subtype1          0
  subtype2          0
  subtype3          1
D3V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  3     3
  subtype2  0  0     4
  subtype3  3  4     4
D3V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  4  3     0
  subtype2  2  1     1
  subtype3  2  6     3
D3V5, multiclass
D3V6, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 0 4
  subtype3 2 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    0    4
  subtype3    2    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        0        2
  MALE          6        4        9
D3V7, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       5        2        7 
 [1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"

Clustering(4) Variable = MIRSEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype2 6 5
  subtype3 6 1
subtype2 subtype3 
      11        7 
subtype2 subtype3 
       5        1 
$subtype2
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.71        29.00         7.10         7.43 

$subtype3
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OM TCGA-LN-A4A2 
        0.03         0.53         0.79         0.36         4.08         0.13 
TCGA-LN-A4A9 
        0.07 

subtype2 subtype3 
    0.26     0.03 
subtype2 subtype3 
   30.71     4.08 
subtype2 subtype3 
    3.68     0.36 
[1] "0.3 - 30.7 (3.7)" "0.0 - 4.1 (0.4)" 
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[1] "hr=" "3.8"
D4V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype2        1        0         1         5          1          2
  subtype3        1        1         2         2          4          1
          vv
clus       STAGE IIIC
  subtype2          1
  subtype3          0
D4V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype2  3  4     4
  subtype3  1  3     7
D4V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype2  2  6     3
  subtype3  6  4     1
D4V5, multiclass
D4V6, binary
          cls
clus        0  1
  subtype2  2  9
  subtype3  1 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    9
  subtype3    1   10
        clus
vv       subtype2 subtype3
  FEMALE        2        1
  MALE          9       10
D4V7, continuous

Clustering(5) Variable = MIRSEQ_MATURE_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 1 0
  subtype3 4 1
  subtype4 5 5
subtype1 subtype3 subtype4 
       1        5       10 
subtype1 subtype3 subtype4 
       0        1        5 
$subtype1
TCGA-IG-A50L 
        0.53 

$subtype3
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.03         0.79         0.36         0.13         0.07 

$subtype4
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.26         3.48        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       30.71        29.00         7.10         7.43 

subtype1 subtype3 subtype4 
    0.53     0.03     0.26 
subtype1 subtype3 subtype4 
    0.53     0.79    30.71 
subtype1 subtype3 subtype4 
    0.53     0.13     5.29 
[1] "0.5 - 0.5 (0.5)"  "0.0 - 0.8 (0.1)"  "0.3 - 30.7 (5.3)"
 [1] "subtype3" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype4" "subtype3" "subtype3"
 [1] "subtype3" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype4" "subtype3" "subtype3"
 [1] "subtype3" "subtype4" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype4" "subtype3" "subtype3"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype3 subtype4 
       1        5       10 
 [1] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype3" "subtype3"
[1] "hr="     "3.6e+09"
D5V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1        0        0         0         0          4          0
  subtype3        0        1         2         2          0          1
  subtype4        1        0         1         4          1          2
          vv
clus       STAGE IIIC
  subtype1          0
  subtype3          0
  subtype4          1
D5V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  0  0     4
  subtype3  0  3     3
  subtype4  2  4     4
D5V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  2  2     0
  subtype3  3  2     1
  subtype4  2  5     3
D5V5, multiclass
D5V6, binary
          cls
clus       0 1
  subtype1 0 4
  subtype3 0 6
  subtype4 2 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype3    0    6
  subtype4    2    8
        clus
vv       subtype1 subtype3 subtype4
  FEMALE        0        0        2
  MALE          4        6        8
D5V7, continuous

Clustering(6) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype2 6 5
  subtype3 6 1
subtype2 subtype3 
      11        7 
subtype2 subtype3 
       5        1 
$subtype2
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.71        29.00         7.10         7.43 

$subtype3
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OM TCGA-LN-A4A2 
        0.03         0.53         0.79         0.36         4.08         0.13 
TCGA-LN-A4A9 
        0.07 

subtype2 subtype3 
    0.26     0.03 
subtype2 subtype3 
   30.71     4.08 
subtype2 subtype3 
    3.68     0.36 
[1] "0.3 - 30.7 (3.7)" "0.0 - 4.1 (0.4)" 
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
 [1] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[1] "hr=" "3.8"
D6V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype2        1        0         1         5          1          2
  subtype3        1        1         2         2          4          1
          vv
clus       STAGE IIIC
  subtype2          1
  subtype3          0
D6V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype2  3  4     4
  subtype3  1  3     7
D6V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype2  2  6     3
  subtype3  6  4     1
D6V5, multiclass
D6V6, binary
          cls
clus        0  1
  subtype2  2  9
  subtype3  1 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    9
  subtype3    1   10
        clus
vv       subtype2 subtype3
  FEMALE        2        1
  MALE          9       10
D6V7, continuous
> q(save="no")
