
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-All_Primary/3157297/1.GDAC_mergedClustering.Finished/SKCM-All_Primary.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Primary/3180571/SKCM-All_Primary.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=31, in cluster file=58, common to both=31
[1]  8 31
[1] "CN_CNMF"
[1] 3
 1  2  3 
10  8 11 
 1  2  3 
10  8 11 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
 4  7 11  5  4 
 1  2  3  4  5 
 4  7 11  5  4 
[1] "RPPA_CNMF"
[1] 3
1 2 3 
6 2 4 
1 3 
6 4 
[1] "RPPA_CHIERARCHICAL"
[1] 3
1 2 3 
4 2 6 
1 3 
4 6 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
16 11 
 1  2 
16 11 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
10  1 16 
 1  3 
10 16 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2 
15 13 
 1  2 
15 13 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 9  6 13 
 1  2  3 
 9  6 13 
[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 31 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 
         237          118           16           13           41           NA 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF 
          39           36            9           NA           NA            4 
TCGA-EB-A3Y6 TCGA-EB-A3Y7 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
          16           NA            8            3            6           12 
TCGA-EB-A430 TCGA-EB-A431 TCGA-EB-A4IQ TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN 
          NA           52           12           NA          307           NA 
TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-HR-A2OG TCGA-HR-A2OH 
           1           NA           NA           NA           NA           NA 
TCGA-IH-A3EA 
         524 
Variable 1:'AGE':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=4,	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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=6,	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
T2A T3A T3B  T4 T4A T4B 
  1   2   1   1   1  24 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 31 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=22, 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=9, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 5 1
  subtype2 7 1
  subtype3 5 3
subtype1 subtype2 subtype3 
       6        8        8 
subtype1 subtype2 subtype3 
       1        1        3 
$subtype1
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A41B TCGA-FR-A2OS 
        7.79         0.43         1.28         0.30         0.10        12.10 

$subtype2
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A42Y TCGA-EB-A42Z 
        3.88         1.35         0.13         0.53         0.20         0.39 
TCGA-FS-A1ZN TCGA-GF-A2C7 
       24.00         0.03 

$subtype3
TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A41A TCGA-FR-A3R1 TCGA-GN-A263 TCGA-GN-A269 
        0.53         1.18         0.26        10.09        15.35         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       26.99        17.23 

subtype1 subtype2 subtype3 
    0.10     0.03     0.26 
subtype1 subtype2 subtype3 
   12.10    24.00    26.99 
subtype1 subtype2 subtype3 
   0.855    0.460    7.840 
[1] "0.1 - 12.1 (0.9)" "0.0 - 24.0 (0.5)" "0.3 - 27.0 (7.8)"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype1" "subtype2" "subtype1"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype2" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3"
D1V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2             7
  subtype2                  0             7
  subtype3                  0            11
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
  subtype3                                                                                        0
D1V3, multiclass
D1V4, binary
          cls
clus       0 1
  subtype1 5 5
  subtype2 2 6
  subtype3 2 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    5
  subtype2    2    6
  subtype3    2    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        2        2
  MALE          5        6        9
          vv
clus       N0 N1A N1B N2A N2B N2C N3 NX
  subtype1  6   0   0   1   1   0  0  1
  subtype2  4   1   1   0   1   0  1  0
  subtype3  5   0   0   0   1   1  2  2
D1V5, multiclass
D1V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        1        0         1         5          0          1
  subtype2        0        0         0         4          1          1
  subtype3        0        1         0         6          0          1
          vv
clus       STAGE IIIC STAGE IV
  subtype1          0        0
  subtype2          2        0
  subtype3          2        1
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 4 0
  subtype2 6 1
  subtype3 3 3
  subtype4 4 0
  subtype5 2 1
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        7        6        4        3 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        1        3        0        1 
$subtype1
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3Y6 TCGA-EB-A41B 
        3.88         1.35         0.53         0.10 

$subtype2
TCGA-D9-A1X3 TCGA-EB-A41A TCGA-EB-A42Y TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GF-A2C7 
        7.79         0.26         0.20        10.09        24.00         0.03 
TCGA-IH-A3EA 
       17.23 

$subtype3
TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A431 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C 
        0.53         1.18         1.71        15.35         5.59        26.99 

$subtype4
TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A42Z 
        1.28         0.30         0.13         0.39 

$subtype5
TCGA-EB-A24C TCGA-EB-A4IQ TCGA-FR-A2OS 
        0.43         0.39        12.10 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.03     0.53     0.13     0.39 
subtype1 subtype2 subtype3 subtype4 subtype5 
    3.88    24.00    26.99     1.28    12.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
   0.940    7.790    3.650    0.345    0.430 
[1] "0.1 - 3.9 (0.9)"  "0.0 - 24.0 (7.8)" "0.5 - 27.0 (3.6)" "0.1 - 1.3 (0.3)" 
[5] "0.4 - 12.1 (0.4)"
 [1] "subtype2" "subtype1" "subtype3" "subtype5" "subtype1" "subtype4"
 [7] "subtype3" "subtype4" "subtype4" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype4" "subtype3" "subtype5" "subtype5" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [1] "subtype2" "subtype1" "subtype3" "subtype5" "subtype1" "subtype4"
 [7] "subtype3" "subtype4" "subtype4" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype4" "subtype3" "subtype5" "subtype5" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [1] "subtype2" "subtype1" "subtype3" "subtype5" "subtype1" "subtype4"
 [7] "subtype3" "subtype4" "subtype4" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype4" "subtype3" "subtype5" "subtype5" "subtype2"
[19] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
D2V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  0             4
  subtype2                  0             5
  subtype3                  2             9
  subtype4                  0             5
  subtype5                  0             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        0
  subtype2                                                                                        2
  subtype3                                                                                        0
  subtype4                                                                                        0
  subtype5                                                                                        0
D2V3, multiclass
D2V4, binary
          cls
clus       0 1
  subtype1 2 2
  subtype2 1 6
  subtype3 4 7
  subtype4 0 5
  subtype5 3 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    2
  subtype2    1    6
  subtype3    4    7
  subtype4    0    5
  subtype5    3    1
          vv
clus       N0 N1 N1A N1B N2A N2B N2C N3 NX
  subtype1  2  0   0   0   0   1   0  1  0
  subtype2  5  0   1   0   0   1   0  0  0
  subtype3  3  0   0   0   1   1   1  2  2
  subtype4  4  0   0   1   0   0   0  0  0
  subtype5  2  1   0   0   0   0   0  0  1
D2V5, multiclass
D2V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        0        0         0         2          0          1
  subtype2        0        0         0         5          1          0
  subtype3        0        1         0         4          0          2
  subtype4        1        0         0         3          0          0
  subtype5        0        0         1         2          0          1
          vv
clus       STAGE IIIC STAGE IV
  subtype1          1        0
  subtype2          0        0
  subtype3          2        1
  subtype4          1        0
  subtype5          0        0
D2V7, multiclass

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 2
  subtype3 1 1
subtype1 subtype3 
       5        2 
subtype1 subtype3 
       2        1 
$subtype1
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A24D TCGA-FS-A1ZN TCGA-GN-A26C 
        7.79         0.43         1.35        24.00        26.99 

$subtype3
TCGA-EB-A1NK TCGA-GN-A269 
        0.53         5.59 

subtype1 subtype3 
    0.43     0.53 
subtype1 subtype3 
   26.99     5.59 
subtype1 subtype3 
    7.79     3.06 
[1] "0.4 - 27.0 (7.8)" "0.5 - 5.6 (3.1)" 
[1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[1] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype3 
       5        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
D3V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  1             4
  subtype3                  1             3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype3                                                                                        0
D3V3, multiclass
D3V4, binary
          cls
clus       0 1
  subtype1 1 5
  subtype3 1 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype3    1    3
        clus
vv       subtype1 subtype3
  FEMALE        1        1
  MALE          5        3
          vv
clus       N0 N1A N2A N2B N3 NX
  subtype1  0   1   1   3  0  1
  subtype3  2   0   0   0  1  0
D3V5, multiclass
D3V6, continuous
          vv
clus       STAGE IB STAGE IIC STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        0         1          1          2          1
  subtype3        1         1          0          0          1
D3V7, multiclass

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 1 1
  subtype3 3 2
subtype1 subtype3 
       2        5 
subtype1 subtype3 
       1        2 
$subtype1
TCGA-EB-A1NK TCGA-GN-A269 
        0.53         5.59 

$subtype3
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A24D TCGA-FS-A1ZN TCGA-GN-A26C 
        7.79         0.43         1.35        24.00        26.99 

subtype1 subtype3 
    0.53     0.43 
subtype1 subtype3 
    5.59    26.99 
subtype1 subtype3 
    3.06     7.79 
[1] "0.5 - 5.6 (3.1)"  "0.4 - 27.0 (7.8)"
[1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[1] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype3 
       2        5 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
D4V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  1             3
  subtype3                  1             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        0
  subtype3                                                                                        1
D4V3, multiclass
D4V4, binary
          cls
clus       0 1
  subtype1 1 3
  subtype3 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype3    1    5
        clus
vv       subtype1 subtype3
  FEMALE        1        1
  MALE          3        5
          vv
clus       N0 N1A N2A N2B N3 NX
  subtype1  2   0   0   0  1  0
  subtype3  0   1   1   3  0  1
D4V5, multiclass
D4V6, continuous
          vv
clus       STAGE IB STAGE IIC STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        1         1          0          0          1
  subtype3        0         1          1          2          1
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 9 3
  subtype2 7 1
subtype1 subtype2 
      12        8 
subtype1 subtype2 
       3        1 
$subtype1
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A3XB TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        7.79         3.88         1.18         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-GN-A263 TCGA-GN-A26C 
        0.20         0.39        12.10        10.09        15.35        26.99 

$subtype2
TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A3XF 
        0.53         0.43         1.35         1.28         0.30         0.13 
TCGA-FS-A1ZN TCGA-GF-A2C7 
       24.00         0.03 

subtype1 subtype2 
    0.10     0.03 
subtype1 subtype2 
   26.99    24.00 
subtype1 subtype2 
    2.53     0.48 
[1] "0.1 - 27.0 (2.5)" "0.0 - 24.0 (0.5)"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[19] "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[19] "subtype1" "subtype1"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[19] "subtype1" "subtype1"
[1] "hr=" "1.1"
D5V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2            13
  subtype2                  0            10
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        1
D5V3, multiclass
D5V4, binary
          cls
clus       0 1
  subtype1 7 9
  subtype2 2 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2    2    9
        clus
vv       subtype1 subtype2
  FEMALE        7        2
  MALE          9        9
          vv
clus       N0 N1A N1B N2A N2B N2C N3 NX
  subtype1  7   0   1   1   2   1  2  1
  subtype2  7   1   0   0   1   0  0  2
D5V5, multiclass
D5V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        0        1         0         7          0          2
  subtype2        1        0         1         7          1          1
          vv
clus       STAGE IIIC STAGE IV
  subtype1          3        1
  subtype2          0        0
D5V7, multiclass

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 6 1
  subtype3 9 3
subtype1 subtype3 
       7       12 
subtype1 subtype3 
       1        3 
$subtype1
TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A3XF TCGA-FS-A1ZN 
        0.53         0.43         1.28         0.30         0.13        24.00 
TCGA-GF-A2C7 
        0.03 

$subtype3
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A3XB TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        7.79         3.88         1.18         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-GN-A263 TCGA-GN-A26C 
        0.20         0.39        12.10        10.09        15.35        26.99 

subtype1 subtype3 
    0.03     0.10 
subtype1 subtype3 
   24.00    26.99 
subtype1 subtype3 
    0.43     2.53 
[1] "0.0 - 24.0 (0.4)" "0.1 - 27.0 (2.5)"
 [1] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype3"
 [1] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype3"
 [1] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype3"
[1] "hr=" "1.1"
D6V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  0             9
  subtype3                  2            13
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype3                                                                                        1
D6V3, multiclass
D6V4, binary
          cls
clus       0 1
  subtype1 2 8
  subtype3 7 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    8
  subtype3    7    9
        clus
vv       subtype1 subtype3
  FEMALE        2        7
  MALE          8        9
          vv
clus       N0 N1A N1B N2A N2B N2C N3 NX
  subtype1  7   1   0   0   0   0  0  2
  subtype3  7   0   1   1   2   1  2  1
D6V5, multiclass
D6V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        1        0         1         7          1          0
  subtype3        0        1         0         7          0          2
          vv
clus       STAGE IIIC STAGE IV
  subtype1          0        0
  subtype3          3        1
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  6  2
subtype1 subtype2 
      13        8 
subtype1 subtype2 
       2        2 
$subtype1
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF 
        7.79         0.43         1.35         1.28         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FS-A1ZN 
        0.53         0.26         0.10         0.39        12.10        24.00 
TCGA-GF-A2C7 
        0.03 

$subtype2
TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A3XC TCGA-EB-A42Y TCGA-FR-A3R1 TCGA-GN-A263 
        3.88         0.53         0.30         0.20        10.09        15.35 
TCGA-GN-A26C TCGA-IH-A3EA 
       26.99        17.23 

subtype1 subtype2 
    0.03     0.20 
subtype1 subtype2 
   24.00    26.99 
subtype1 subtype2 
   0.530    6.985 
[1] "0.0 - 24.0 (0.5)" "0.2 - 27.0 (7.0)"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[19] "subtype2" "subtype2" "subtype2"
[1] "hr=" "3.4"
D7V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  0            13
  subtype2                  2            11
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        2
  subtype2                                                                                        0
D7V3, multiclass
D7V4, binary
          cls
clus        0  1
  subtype1  5 10
  subtype2  4  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   10
  subtype2    4    9
        clus
vv       subtype1 subtype2
  FEMALE        5        4
  MALE         10        9
          vv
clus       N0 N1A N1B N2A N2B N2C N3 NX
  subtype1  8   1   1   0   2   1  0  2
  subtype2  7   0   0   1   1   0  2  1
D7V5, multiclass
D7V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        0        1         1         8          1          2
  subtype2        1        0         0         7          0          1
          vv
clus       STAGE IIIC STAGE IV
  subtype1          1        0
  subtype2          2        1
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 4 2
  subtype2 4 1
  subtype3 9 1
subtype1 subtype2 subtype3 
       6        5       10 
subtype1 subtype2 subtype3 
       2        1        1 
$subtype1
TCGA-EB-A1NK TCGA-EB-A24C TCGA-FR-A2OS TCGA-GF-A2C7 TCGA-GN-A263 TCGA-IH-A3EA 
        0.53         0.43        12.10         0.03        15.35        17.23 

$subtype2
TCGA-D9-A3Z4 TCGA-EB-A3XC TCGA-EB-A42Y TCGA-FR-A3R1 TCGA-GN-A26C 
        3.88         0.30         0.20        10.09        26.99 

$subtype3
TCGA-D9-A1X3 TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 
        7.79         1.35         1.28         1.18         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-FS-A1ZN 
        0.26         0.10         0.39        24.00 

subtype1 subtype2 subtype3 
    0.03     0.20     0.10 
subtype1 subtype2 subtype3 
   17.23    26.99    24.00 
subtype1 subtype2 subtype3 
   6.315    3.880    0.855 
[1] "0.0 - 17.2 (6.3)" "0.2 - 27.0 (3.9)" "0.1 - 24.0 (0.9)"
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1"
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1"
 [1] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype1"
D8V2, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  1             7
  subtype2                  1             5
  subtype3                  0            12
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  subtype1                                                                                        1
  subtype2                                                                                        0
  subtype3                                                                                        1
D8V3, multiclass
D8V4, binary
          cls
clus       0 1
  subtype1 3 6
  subtype2 2 4
  subtype3 4 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    2    4
  subtype3    4    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        2        4
  MALE          6        4        9
          vv
clus       N0 N1A N1B N2A N2B N2C N3 NX
  subtype1  5   0   0   1   0   1  1  1
  subtype2  3   0   0   0   1   0  1  0
  subtype3  7   1   1   0   2   0  0  2
D8V5, multiclass
D8V6, continuous
          vv
clus       STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  subtype1        0        0         0         6          0          2
  subtype2        0        0         0         3          0          0
  subtype3        1        1         1         6          1          1
          vv
clus       STAGE IIIC STAGE IV
  subtype1          0        1
  subtype2          2        0
  subtype3          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")
