
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/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2843106/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=40, in cluster file=134, common to both=40
[1]  6 40
[1] "CN_CNMF"
[1] 3
 1  2  3 
17  5 12 
 1  2  3 
17  5 12 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
24 12  4 
 1  2  3 
24 12  4 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
21 10  5 
 1  2  3 
21 10  5 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 6 26  4 
 1  2  3 
 6 26  4 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
15 15 10 
 1  2  3 
15 15 10 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 5 22 13 
 1  2  3 
 5 22 13 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "TOBACCOSMOKINGHISTORYINDICATOR"        
[13] "DISTANT.METASTASIS"                    
[14] "LYMPH.NODE.METASTASIS"                 
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 40 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
        1505          925         5385           NA           NA         1616 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
          NA           NA           NA         2382         2155         1289 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA 
          NA           81         2127         2892           NA           NA 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
          NA          376         3096          183            8           53 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EK-A2PI TCGA-EX-A1H5 
          40           25           19           81           NA          178 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
         211           37           37           30           66            2 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
          31           44          773          168 
Variable 1:'AGE':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "NUMBERPACKYEARSSMOKED"                 
[5] "TOBACCOSMOKINGHISTORYINDICATOR"        
[6] "DISTANT.METASTASIS"                    
[7] "LYMPH.NODE.METASTASIS"                 
[8] "NUMBER.OF.LYMPH.NODES"                 
[9] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B   T4 
   5   13    5    2    2    2    5    1    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 40 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=30, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=9, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 14  2
  subtype2  2  3
  subtype3 11  1
subtype1 subtype2 subtype3 
      16        5       12 
subtype1 subtype2 subtype3 
       2        3        1 
$subtype1
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A2LY TCGA-DS-A0VK 
       49.48        30.41        67.46        53.13        78.31        36.76 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66         6.02         0.26         1.74         1.32         0.82 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A3JK 
        5.85         1.22         1.45         5.52 

$subtype2
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VM 
        5.46        35.61        40.93        70.85        69.93 

$subtype3
TCGA-C5-A1BK TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-EA-A3HT TCGA-EX-A3L1 
      177.04         2.43        42.38        95.08         0.62         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.22         0.99         2.17         0.07         1.02        25.41 

subtype1 subtype2 subtype3 
    0.26     5.46     0.07 
subtype1 subtype2 subtype3 
   78.31    70.85   177.04 
subtype1 subtype2 subtype3 
   5.685   40.930    2.300 
[1] "0.3 - 78.3 (5.7)"  "5.5 - 70.8 (40.9)" "0.1 - 177.0 (2.3)"
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype3" "subtype1"
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
 [7] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[13] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype1" "subtype3" "subtype1"
D1V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                               14                                   0
  subtype2                                5                                   0
  subtype3                                8                                   1
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       3
  subtype2                       0
  subtype3                       3
D1V3, multiclass
D1V4, binary
          cls
clus        0  1
  subtype1  5 12
  subtype2  3  2
  subtype3  3  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   12
  subtype2    3    2
  subtype3    3    9
     clus
vv    subtype1 subtype2 subtype3
  NO         5        3        3
  YES       12        2        9
D1V5, continuous
D1V6, continuous
D1V7, binary
          cls
clus        0  1
  subtype1 11  5
  subtype2  3  0
  subtype3  6  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    5
  subtype2    3    0
  subtype3    6    4
    clus
vv   subtype1 subtype2 subtype3
  M0       11        3        6
  MX        5        0        4
D1V8, binary
          cls
clus        0  1
  subtype1 10  6
  subtype2  1  2
  subtype3  8  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    6
  subtype2    1    2
  subtype3    8    3
    clus
vv   subtype1 subtype2 subtype3
  N0       10        1        8
  N1        6        2        3
D1V9, continuous
D1V10, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16  7
  subtype2 10  2
  subtype3  4  0
subtype1 subtype2 subtype3 
      23       12        4 
subtype1 subtype2 subtype3 
       7        2        0 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MN TCGA-DS-A0VK 
       49.48       177.04         5.46        67.46        40.93        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB 
        2.66        69.93        95.08         8.75        28.90        28.27 
TCGA-DS-A1OC TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       12.36         6.02         0.26         1.74         1.32         0.82 
TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-HM-A3JK 
        5.85         0.99         0.07         1.45         5.52 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       30.41        35.61         2.43        78.31        70.85        42.38 
TCGA-DS-A1OD TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A3L1 TCGA-FU-A23L TCGA-HG-A2PA 
      101.79         0.62         2.66         6.94         1.22        25.41 

$subtype3
TCGA-C5-A1MF TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
       53.13         1.22         2.17         1.02 

subtype1 subtype2 subtype3 
    0.07     0.62     1.02 
subtype1 subtype2 subtype3 
  177.04   101.79    53.13 
subtype1 subtype2 subtype3 
   6.020   27.910    1.695 
[1] "0.1 - 177.0 (6.0)"  "0.6 - 101.8 (27.9)" "1.0 - 53.1 (1.7)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[37] "subtype1" "subtype2" "subtype1"
D2V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                               20                                   0
  subtype2                               10                                   0
  subtype3                                3                                   1
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       4
  subtype2                       2
  subtype3                       0
D2V3, multiclass
D2V4, binary
          cls
clus        0  1
  subtype1  9 15
  subtype2  5  7
  subtype3  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   15
  subtype2    5    7
  subtype3    1    3
     clus
vv    subtype1 subtype2 subtype3
  NO         9        5        1
  YES       15        7        3
D2V5, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       6        2        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
D2V6, continuous
D2V7, binary
          cls
clus        0  1
  subtype1 15  5
  subtype2 10  1
  subtype3  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    5
  subtype2   10    1
  subtype3    1    3
    clus
vv   subtype1 subtype2 subtype3
  M0       15       10        1
  MX        5        1        3
D2V8, binary
          cls
clus        0  1
  subtype1 10 11
  subtype2  9  2
  subtype3  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   11
  subtype2    9    2
  subtype3    3    1
    clus
vv   subtype1 subtype2 subtype3
  N0       10        9        3
  N1       11        2        1
D2V9, continuous
D2V10, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 18  3
  subtype2  6  3
  subtype3  4  1
subtype1 subtype2 subtype3 
      21        9        5 
subtype1 subtype2 subtype3 
       3        3        1 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-DR-A0ZM 
       49.48       177.04        67.46         2.43        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A1H5 TCGA-FU-A23L 
        1.32         0.82         0.62         2.66         5.85         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI 
        0.99         0.07         1.45 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VM TCGA-DS-A1OB 
       30.41         5.46        40.93        78.31        69.93        28.27 
TCGA-DS-A1OC TCGA-DS-A1OD TCGA-FU-A3HZ 
       12.36       101.79         1.02 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-FU-A23K TCGA-FU-A3EO TCGA-HG-A2PA 
       53.13        35.61         1.22         2.17        25.41 

subtype1 subtype2 subtype3 
    0.07     1.02     1.22 
subtype1 subtype2 subtype3 
  177.04   101.79    53.13 
subtype1 subtype2 subtype3 
    2.66    30.41    25.41 
[1] "0.1 - 177.0 (2.7)"  "1.0 - 101.8 (30.4)" "1.2 - 53.1 (25.4)" 
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
D3V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                               17                                   0
  subtype2                               10                                   0
  subtype3                                4                                   1
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       4
  subtype2                       0
  subtype3                       0
D3V3, multiclass
D3V4, binary
          cls
clus        0  1
  subtype1  5 16
  subtype2  6  4
  subtype3  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   16
  subtype2    6    4
  subtype3    2    3
     clus
vv    subtype1 subtype2 subtype3
  NO         5        6        2
  YES       16        4        3
D3V5, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       5        2        3 
[1] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[8] "subtype1"
D3V6, continuous
D3V7, binary
          cls
clus        0  1
  subtype1 14  5
  subtype2  7  0
  subtype3  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    5
  subtype2    7    0
  subtype3    2    3
    clus
vv   subtype1 subtype2 subtype3
  M0       14        7        2
  MX        5        0        3
D3V8, binary
          cls
clus        0  1
  subtype1 13  7
  subtype2  4  3
  subtype3  3  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    7
  subtype2    4    3
  subtype3    3    2
    clus
vv   subtype1 subtype2 subtype3
  N0       13        4        3
  N1        7        3        2
D3V9, continuous
D3V10, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5  0
  subtype2 20  6
  subtype3  3  1
subtype1 subtype2 subtype3 
       5       26        4 
subtype1 subtype2 subtype3 
       0        6        1 
$subtype1
TCGA-BI-A0VS TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-FU-A3HZ 
       30.41        12.36       101.79         6.02         1.02 

$subtype2
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-C5-A1MN 
       49.48       177.04         5.46        67.46         2.43        40.93 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       78.31        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A1OB TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       95.08        28.27         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        0.62         2.66         5.85         1.22         0.99         0.07 
TCGA-FU-A3NI TCGA-HG-A2PA 
        1.45        25.41 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-FU-A23K TCGA-FU-A3EO 
       53.13        35.61         1.22         2.17 

subtype1 subtype2 subtype3 
    1.02     0.07     1.22 
subtype1 subtype2 subtype3 
  101.79   177.04    53.13 
subtype1 subtype2 subtype3 
  12.360    5.655   18.890 
[1] "1.0 - 101.8 (12.4)" "0.1 - 177.0 (5.7)"  "1.2 - 53.1 (18.9)" 
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[19] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
D4V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                5                                   0
  subtype2                               23                                   0
  subtype3                                3                                   1
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       1
  subtype2                       3
  subtype3                       0
D4V3, multiclass
D4V4, binary
          cls
clus        0  1
  subtype1  3  3
  subtype2  8 18
  subtype3  2  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    8   18
  subtype3    2    2
     clus
vv    subtype1 subtype2 subtype3
  NO         3        8        2
  YES        3       18        2
D4V5, continuous
D4V6, continuous
D4V7, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 17  5
  subtype3  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   17    5
  subtype3    1    3
    clus
vv   subtype1 subtype2 subtype3
  M0        5       17        1
  MX        0        5        3
D4V8, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 15  8
  subtype3  2  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   15    8
  subtype3    2    2
    clus
vv   subtype1 subtype2 subtype3
  N0        3       15        2
  N1        2        8        2
D4V9, continuous
D4V10, continuous

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 10  5
  subtype2 11  3
  subtype3  9  1
subtype1 subtype2 subtype3 
      15       14       10 
subtype1 subtype2 subtype3 
       5        3        1 
$subtype1
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL 
       49.48       177.04         5.46         2.43        40.93        70.85 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OB TCGA-DS-A1OC 
        2.66        69.93        95.08         8.75        28.27        12.36 
TCGA-EA-A1QT TCGA-EX-A3L1 TCGA-FU-A3HY 
        0.26         6.94         0.07 

$subtype2
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A1OA TCGA-DS-A1OD 
       30.41        67.46        42.38        36.76        28.90       101.79 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-FU-A3EO TCGA-FU-A3NI 
        1.74         1.32         0.82         0.62         2.17         1.45 
TCGA-HG-A2PA TCGA-HM-A3JK 
       25.41         5.52 

$subtype3
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A2LY TCGA-DS-A3LQ TCGA-EA-A3HU TCGA-EX-A1H5 
       53.13        35.61        78.31         6.02         2.66         5.85 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HZ 
        1.22         1.22         0.99         1.02 

subtype1 subtype2 subtype3 
    0.07     0.62     0.99 
subtype1 subtype2 subtype3 
  177.04   101.79    78.31 
subtype1 subtype2 subtype3 
  12.360   15.465    4.255 
[1] "0.1 - 177.0 (12.4)" "0.6 - 101.8 (15.5)" "1.0 - 78.3 (4.3)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
D5V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                               13                                   0
  subtype2                               11                                   1
  subtype3                                9                                   0
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       2
  subtype2                       3
  subtype3                       1
D5V3, multiclass
D5V4, binary
          cls
clus        0  1
  subtype1  6  9
  subtype2  4 11
  subtype3  5  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    9
  subtype2    4   11
  subtype3    5    5
     clus
vv    subtype1 subtype2 subtype3
  NO         6        4        5
  YES        9       11        5
D5V5, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        2        4 
[1] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[8] "subtype1"
D5V6, continuous
D5V7, binary
          cls
clus        0  1
  subtype1 10  2
  subtype2 11  3
  subtype3  5  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    2
  subtype2   11    3
  subtype3    5    4
    clus
vv   subtype1 subtype2 subtype3
  M0       10       11        5
  MX        2        3        4
D5V8, binary
          cls
clus       0 1
  subtype1 7 5
  subtype2 9 5
  subtype3 6 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    5
  subtype2    9    5
  subtype3    6    4
    clus
vv   subtype1 subtype2 subtype3
  N0        7        9        6
  N1        5        5        4
D5V9, continuous
D5V10, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  4  1
  subtype2 16  6
  subtype3 10  2
subtype1 subtype2 subtype3 
       5       22       12 
subtype1 subtype2 subtype3 
       1        6        2 
$subtype1
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DS-A3LQ TCGA-FU-A23K TCGA-FU-A3EO 
       53.13        35.61         6.02         1.22         2.17 

$subtype2
TCGA-BI-A0VR TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL 
       49.48       177.04        67.46         2.43        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB 
       42.38        36.76         2.66         8.75        28.90        28.27 
TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
      101.79         0.26         1.74         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        5.85         1.45        25.41         5.52 

$subtype3
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MN TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OC 
       30.41         5.46        40.93        69.93        95.08        12.36 
TCGA-EA-A3HU TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        2.66         6.94         1.22         0.99         0.07         1.02 

subtype1 subtype2 subtype3 
    1.22     0.26     0.07 
subtype1 subtype2 subtype3 
   53.13   177.04    95.08 
subtype1 subtype2 subtype3 
    6.02    17.08     6.20 
[1] "1.2 - 53.1 (6.0)"   "0.3 - 177.0 (17.1)" "0.1 - 95.1 (6.2)"  
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[37] "subtype2" "subtype2" "subtype2"
D6V2, continuous
          vv
clus       CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL TYPE OF ADENOCARCINOMA
  subtype1                                3                                   1
  subtype2                               19                                   0
  subtype3                               11                                   0
          vv
clus       SQUAMOUS CELL CARCINOMA
  subtype1                       1
  subtype2                       3
  subtype3                       2
D6V3, multiclass
D6V4, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2  8 14
  subtype3  4  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    8   14
  subtype3    4    9
     clus
vv    subtype1 subtype2 subtype3
  NO         3        8        4
  YES        2       14        9
D6V5, continuous
D6V6, continuous
D6V7, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2 17  4
  subtype3  7  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2   17    4
  subtype3    7    2
    clus
vv   subtype1 subtype2 subtype3
  M0        2       17        7
  MX        3        4        2
D6V8, binary
          cls
clus        0  1
  subtype1  2  3
  subtype2 13  8
  subtype3  7  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2   13    8
  subtype3    7    3
    clus
vv   subtype1 subtype2 subtype3
  N0        2       13        7
  N1        3        8        3
D6V9, continuous
D6V10, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                     "HISTOLOGICAL.TYPE" 
                                      V4 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V5 
                 "NUMBERPACKYEARSSMOKED" 
                                      V6 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
                                      V7 
                    "DISTANT.METASTASIS" 
                                      V8 
                 "LYMPH.NODE.METASTASIS" 
                                      V9 
                 "NUMBER.OF.LYMPH.NODES" 
                                     V10 
                       "TUMOR.STAGECODE" 
> q(save="no")
