
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.84.4098/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.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-NF1_Any_Mutants/3157448/1.GDAC_mergedClustering.Finished/SKCM-NF1_Any_Mutants.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NF1_Any_Mutants/3215661/SKCM-NF1_Any_Mutants.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=25, in cluster file=31, common to both=25
[1]  8 25
[1] "CN_CNMF"
[1] 3
 1  2 
11 14 
 1  2 
11 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2 
10 15 
 1  2 
10 15 
[1] "RPPA_CNMF"
[1] 3
 1  2 
 6 15 
 1  2 
 6 15 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2 
 3 18 
 1  2 
 3 18 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
 5  9 11 
 1  2  3 
 5  9 11 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 
4 7 6 8 
1 2 3 4 
4 7 6 8 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2 
11 14 
 1  2 
11 14 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
1 4 2 4 8 6 
2 4 5 6 
4 4 8 6 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 25 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
         939           NA           NA           NA           NA           NA 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO 
          NA           NA           NA          727           NA           NA 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
          NA           NA           NA           NA           NA            6 
TCGA-GN-A266 
          NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T2A  T3 T3A T3B  T4 T4B  TX 
  3   1   2   2   4   2   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 2 5
  subtype2 1 5
subtype1 subtype2 
       7        6 
subtype1 subtype2 
       5        5 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 
       30.87        10.03        11.57         1.12         9.47        23.90 
TCGA-GN-A266 
       10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        6.64         1.35         1.08         2.43        11.11         0.20 

subtype1 subtype2 
    1.12     0.20 
subtype1 subtype2 
   30.87    11.11 
subtype1 subtype2 
   10.09     1.89 
[1] "1.1 - 30.9 (10.1)" "0.2 - 11.1 (1.9)" 
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1"
[1] "hr=" "3.4"
D1V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  1
  subtype2                  6
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   8
  subtype2                   5
D1V3, multiclass
D1V4, binary
          cls
clus       0 1
  subtype1 2 9
  subtype2 6 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    9
  subtype2    6    8
        clus
vv       subtype1 subtype2
  FEMALE        2        6
  MALE          9        8
          vv
clus       N0 N1B N2C N3
  subtype1  8   1   0  1
  subtype2  8   2   2  1
D1V5, multiclass
D1V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        3        0        3         1          1          1        0
  subtype2        0        1        3         2          2          3        1
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 1 5
  subtype2 2 5
subtype1 subtype2 
       6        7 
subtype1 subtype2 
       5        5 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V TCGA-GN-A266 
       30.87        10.03         1.12         9.47         2.43        10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19F 
        6.64        11.57         1.35         1.08        23.90        11.11 
TCGA-FW-A3I3 
        0.20 

subtype1 subtype2 
    1.12     0.20 
subtype1 subtype2 
   30.87    23.90 
subtype1 subtype2 
    9.75     6.64 
[1] "1.1 - 30.9 (9.8)" "0.2 - 23.9 (6.6)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1"
[1] "hr=" "1.2"
D2V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  5
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   6
  subtype2                   7
D2V3, multiclass
D2V4, binary
          cls
clus       0 1
  subtype1 1 9
  subtype2 7 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    7    8
        clus
vv       subtype1 subtype2
  FEMALE        1        7
  MALE          9        8
          vv
clus       N0 N1B N2C N3
  subtype1  7   1   0  1
  subtype2  9   2   2  1
D2V5, multiclass
D2V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        1        1        3         1          0          2        0
  subtype2        2        0        3         2          3          2        1
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 0 4
  subtype2 1 5
subtype1 subtype2 
       4        6 
subtype1 subtype2 
       4        5 
$subtype1
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
        6.64         1.35         9.47         2.43 

$subtype2
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19F TCGA-GN-A266 
       11.57         1.12         1.08        23.90        11.11        10.09 

subtype1 subtype2 
    1.35     1.08 
subtype1 subtype2 
    9.47    23.90 
subtype1 subtype2 
   4.535   10.600 
[1] "1.4 - 9.5 (4.5)"   "1.1 - 23.9 (10.6)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
[1] "hr=" "3.4"
D3V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  4
  subtype2                  1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   1
  subtype2                  12
D3V3, multiclass
D3V4, binary
          cls
clus        0  1
  subtype1  3  3
  subtype2  3 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    3   12
        clus
vv       subtype1 subtype2
  FEMALE        3        3
  MALE          3       12
          vv
clus       N0 N1B N2C N3
  subtype1  2   2   2  0
  subtype2 11   1   0  1
D3V5, multiclass
D3V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  subtype1        0        0        0         1          2          2
  subtype2        2        1        5         2          1          1
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 0 3
  subtype2 1 6
subtype1 subtype2 
       3        7 
subtype1 subtype2 
       3        6 
$subtype1
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29V 
        6.64         1.35         2.43 

$subtype2
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 TCGA-ER-A19F 
       11.57         1.12         1.08         9.47        23.90        11.11 
TCGA-GN-A266 
       10.09 

subtype1 subtype2 
    1.35     1.08 
subtype1 subtype2 
    6.64    23.90 
subtype1 subtype2 
    2.43    10.09 
[1] "1.4 - 6.6 (2.4)"   "1.1 - 23.9 (10.1)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2"
[1] "hr=" "3.8"
D4V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   0
  subtype2                  13
D4V3, multiclass
D4V4, binary
          cls
clus        0  1
  subtype1  1  2
  subtype2  5 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    5   13
        clus
vv       subtype1 subtype2
  FEMALE        1        5
  MALE          2       13
          vv
clus       N0 N1B N2C N3
  subtype1  0   2   1  0
  subtype2 13   1   1  1
D4V5, multiclass
D4V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  subtype1        0        0        0         0          1          2
  subtype2        2        1        5         3          2          1
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype2 2 3
  subtype3 1 7
subtype2 subtype3 
       5        8 
subtype2 subtype3 
       3        7 
$subtype2
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 TCGA-GN-A266 
       30.87         1.12         9.47        23.90        10.09 

$subtype3
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       10.03         6.64        11.57         1.35         1.08         2.43 
TCGA-ER-A19F TCGA-FW-A3I3 
       11.11         0.20 

subtype2 subtype3 
    1.12     0.20 
subtype2 subtype3 
   30.87    11.57 
subtype2 subtype3 
  10.090    4.535 
[1] "1.1 - 30.9 (10.1)" "0.2 - 11.6 (4.5)" 
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[13] "subtype2"
[1] "hr=" "2.4"
D5V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  1
  subtype3                  4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
  subtype3                                                                                        3
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   2
  subtype2                   7
  subtype3                   4
D5V3, multiclass
D5V4, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 2 7
  subtype3 3 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    2    7
  subtype3    3    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        2        3
  MALE          2        7        8
          vv
clus       N0 N1B N2C N3
  subtype1  3   0   1  0
  subtype2  7   1   0  0
  subtype3  6   2   1  2
D5V5, multiclass
D5V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        0        0        2         1          1          0        0
  subtype2        2        0        3         1          1          0        0
  subtype3        1        1        1         1          1          4        1
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 1 1
  subtype2 1 2
  subtype3 1 5
  subtype4 0 2
subtype1 subtype2 subtype3 subtype4 
       2        3        6        2 
subtype1 subtype2 subtype3 subtype4 
       1        2        5        2 
$subtype1
TCGA-D3-A2JF TCGA-GN-A266 
       30.87        10.09 

$subtype2
TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 
        1.12         9.47        23.90 

$subtype3
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-FW-A3I3 
       10.03         6.64        11.57         1.35         2.43         0.20 

$subtype4
TCGA-EE-A29L TCGA-ER-A19F 
        1.08        11.11 

subtype1 subtype2 subtype3 subtype4 
   10.09     1.12     0.20     1.08 
subtype1 subtype2 subtype3 subtype4 
   30.87    23.90    11.57    11.11 
subtype1 subtype2 subtype3 subtype4 
  20.480    9.470    4.535    6.095 
[1] "10.1 - 30.9 (20.5)" "1.1 - 23.9 (9.5)"   "0.2 - 11.6 (4.5)"  
[4] "1.1 - 11.1 (6.1)"  
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype4" "subtype3"
[13] "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype4" "subtype3"
[13] "subtype1"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype4" "subtype2" "subtype3" "subtype2" "subtype4" "subtype3"
[13] "subtype1"
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        3        6        2 
[1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[8] "subtype2" "subtype3"
[1] "hr=" "1.6"
D6V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  2
  subtype2                  0
  subtype3                  3
  subtype4                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        0
  subtype3                                                                                        2
  subtype4                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   1
  subtype2                   7
  subtype3                   1
  subtype4                   4
D6V3, multiclass
D6V4, binary
          cls
clus       0 1
  subtype1 1 3
  subtype2 2 5
  subtype3 2 4
  subtype4 3 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    2    5
  subtype3    2    4
  subtype4    3    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        2        3
  MALE          3        5        4        5
          vv
clus       N0 N1B N2C N3
  subtype1  2   0   1  0
  subtype2  6   1   0  0
  subtype3  2   2   1  1
  subtype4  6   0   0  1
D6V5, multiclass
D6V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        1        0        0         1          1          0        0
  subtype2        1        0        3         1          1          0        0
  subtype3        1        0        0         0          1          3        1
  subtype4        0        1        3         1          0          1        0
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 2 6
  subtype2 1 4
subtype1 subtype2 
       8        5 
subtype1 subtype2 
       6        4 
$subtype1
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
       30.87        10.03        11.57         1.35         9.47         2.43 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$subtype2
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19F 
        6.64         1.12         1.08        23.90        11.11 

subtype1 subtype2 
    0.20     1.08 
subtype1 subtype2 
   30.87    23.90 
subtype1 subtype2 
    9.75     6.64 
[1] "0.2 - 30.9 (9.8)" "1.1 - 23.9 (6.6)"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype1"
[1] "hr=" "1.2"
D7V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype1                  5
  subtype2                  2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        3
  subtype2                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype1                   3
  subtype2                  10
D7V3, multiclass
D7V4, binary
          cls
clus        0  1
  subtype1  4  7
  subtype2  4 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    7
  subtype2    4   10
        clus
vv       subtype1 subtype2
  FEMALE        4        4
  MALE          7       10
          vv
clus       N0 N1B N2C N3
  subtype1  6   2   1  1
  subtype2 10   1   1  1
D7V5, multiclass
D7V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype1        2        0        1         1          1          3        1
  subtype2        1        1        5         2          2          1        0
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype2 0 1
  subtype4 2 2
  subtype5 0 3
  subtype6 0 2
subtype2 subtype4 subtype5 subtype6 
       1        4        3        2 
subtype2 subtype4 subtype5 subtype6 
       1        2        3        2 
$subtype2
TCGA-GN-A266 
       10.09 

$subtype4
TCGA-DA-A1I0 TCGA-EE-A182 TCGA-EE-A2A2 TCGA-FW-A3I3 
       10.03         1.35        23.90         0.20 

$subtype5
TCGA-EE-A181 TCGA-EE-A29L TCGA-ER-A19F 
        1.12         1.08        11.11 

$subtype6
TCGA-DA-A1IC TCGA-EE-A29V 
        6.64         2.43 

subtype2 subtype4 subtype5 subtype6 
   10.09     0.20     1.08     2.43 
subtype2 subtype4 subtype5 subtype6 
   10.09    23.90    11.11     6.64 
subtype2 subtype4 subtype5 subtype6 
  10.090    5.690    1.120    4.535 
[1] "10.1 - 10.1 (10.1)" "0.2 - 23.9 (5.7)"   "1.1 - 11.1 (1.1)"  
[4] "2.4 - 6.6 (4.5)"   
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype4" "subtype2"
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype4" "subtype2"
 [1] "subtype4" "subtype6" "subtype5" "subtype4" "subtype5" "subtype6"
 [7] "subtype4" "subtype5" "subtype4" "subtype2"
[1] "Remove cluster labels:" "subtype2"               "subtype6"              
clus
subtype2 subtype4 subtype5 subtype6 
       1        4        3        2 
[1] "subtype4" "subtype5" "subtype4" "subtype5" "subtype4" "subtype5" "subtype4"
[1] "hr=" "2.4"
D8V2, continuous
          vv
clus       DISTANT METASTASIS
  subtype2                  1
  subtype4                  2
  subtype5                  2
  subtype6                  1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype2                                                                                        2
  subtype4                                                                                        1
  subtype5                                                                                        0
  subtype6                                                                                        2
          vv
clus       REGIONAL LYMPH NODE
  subtype2                   1
  subtype4                   1
  subtype5                   6
  subtype6                   3
D8V3, multiclass
D8V4, binary
          cls
clus       0 1
  subtype2 2 2
  subtype4 2 2
  subtype5 4 4
  subtype6 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    2
  subtype4    2    2
  subtype5    4    4
  subtype6    0    6
        clus
vv       subtype2 subtype4 subtype5 subtype6
  FEMALE        2        2        4        0
  MALE          2        2        4        6
          vv
clus       N0 N1B N2C N3
  subtype2  2   0   1  0
  subtype4  1   2   0  1
  subtype5  6   0   0  1
  subtype6  4   1   1  0
D8V5, multiclass
D8V6, continuous
          vv
clus       STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC STAGE IV
  subtype2        0        0        1         1          1          0        0
  subtype4        0        0        0         0          1          2        1
  subtype5        1        0        2         2          0          1        0
  subtype6        0        1        3         0          1          1        0
D8V7, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"   "LYMPH.NODE.METASTASIS"         "TUMOR.STAGECODE" 
                       V7 
  "NEOPLASM.DISEASESTAGE" 
> q(save="no")
