
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.36.3689/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.36.3689/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/303455/THCA-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2332309/1.GDAC_clinicalDataPicker.Finished/THCA-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-nV=Nozzle.R1", "-OP=MUTSIG", "-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=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=218, in cluster file=323, common to both=201
[1] "Reduce the number of clustering variables from 45 to 17."
[1]  17 201
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           115             86 
  BRAF MUTATED BRAF WILD-TYPE 
           115             86 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            16            185 
  NRAS MUTATED NRAS WILD-TYPE 
            16            185 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            10            191 
  HRAS MUTATED HRAS WILD-TYPE 
            10            191 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               3              198 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               3              198 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            197 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            197 
[1] "TG MUTATION ANALYSIS"
[1] 3
  TG MUTATED TG WILD-TYPE 
           9          192 
  TG MUTATED TG WILD-TYPE 
           9          192 
[1] "ZNF845 MUTATION ANALYSIS"
[1] 3
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               3              198 
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               3              198 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             196 
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             196 
[1] "ZNF799 MUTATION ANALYSIS"
[1] 3
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               3              198 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               3              198 
[1] "CCDC15 MUTATION ANALYSIS"
[1] 3
  CCDC15 MUTATED CCDC15 WILD-TYPE 
               5              196 
  CCDC15 MUTATED CCDC15 WILD-TYPE 
               5              196 
[1] "COL5A3 MUTATION ANALYSIS"
[1] 3
  COL5A3 MUTATED COL5A3 WILD-TYPE 
               4              197 
  COL5A3 MUTATED COL5A3 WILD-TYPE 
               4              197 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              4             197 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              4             197 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               4              197 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               4              197 
[1] "FAM155A MUTATION ANALYSIS"
[1] 3
  FAM155A MUTATED FAM155A WILD-TYPE 
                3               198 
  FAM155A MUTATED FAM155A WILD-TYPE 
                3               198 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             3            198 
  KRAS MUTATED KRAS WILD-TYPE 
             3            198 
[1] "R3HDM2 MUTATION ANALYSIS"
[1] 3
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               3              198 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               3              198 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
               5              196 
  ARID1B MUTATED ARID1B WILD-TYPE 
               5              196 
[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] "RADIATIONEXPOSURE"                     
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 201 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         479          356          232          182          197          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG 
         264          122          183          237          210          230 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
          22          152           85           13          235          246 
TCGA-BJ-A28R TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-CE-A13K 
         148           84          155          244          367           16 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
           3            6            7          402          231          952 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
         161          286          274          215         4199           92 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
         265          758          393          362          454          243 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
         334         3041          549          212          243          151 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
         212           30          273           31          181          304 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
         242          152          623          318           59          292 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
         312          242          234          153          267          256 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         247          284          206          280          287          301 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
         262          291          215          315          378          330 
TCGA-DJ-A2QC TCGA-DJ-A3UN TCGA-DJ-A3US TCGA-DJ-A3UY TCGA-DO-A1JZ TCGA-DO-A1K0 
         304          380          630          405         1225           93 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
         945          365         1544         1222         1421          635 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
         427           34           11          580          153          214 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
          NA          245          217          284         1421         1209 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
         650           81          207          202          138          106 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
         209          189          174          192          348          249 
TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
         209          357          344          183           90          199 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
         218          319          176         1088           10          903 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
         589          135          621          579          373         1049 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
         449           43         1182            9          362         2058 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
          59         2266         2535         1309          406         1413 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
          20          237           51          177          127           74 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
         168          752           39           56           72          137 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
        2095         1536         1366           65            9          145 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
         138         3424          751         1565         1442          374 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
        1346          751         1333         3130         2031         2292 
TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FY-A2QD TCGA-FY-A3BL 
        1907         2589         1868         1913           38           35 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
          50           30           NA           18           46           23 
TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
           1           66          278          206          106          145 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
         148           90         1070          939           80           99 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
          68          392          415 
Variable 1:'AGE':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=177,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "RADIATIONEXPOSURE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 201 columns, 0 survival variables, and 5 non-survival variables.
AGE, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BRAF MUTATION ANALYSIS
D1V1, continuous
D1V2, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     83   32
  BRAF WILD-TYPE   66   20
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           83             66
  MALE             32             20
D1V3, multiclass
                                                                        clus
vv                                                                       BRAF MUTATED
  OTHER                                                                             1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                    84
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              19
                                                                        clus
vv                                                                       BRAF WILD-TYPE
  OTHER                                                                               7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      24
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             53
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 2
D1V4, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11  104
  BRAF WILD-TYPE    1   85
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            11              1
  YES          104             85
D1V5, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     97    6
  BRAF WILD-TYPE   69    3
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            97             69
  YES            6              3

Clustering(2) Variable = NRAS MUTATION ANALYSIS
D2V1, continuous
D2V2, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      9    7
  NRAS WILD-TYPE  140   45
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            9            140
  MALE              7             45
D2V3, multiclass
                                                                        clus
vv                                                                       NRAS MUTATED
  OTHER                                                                             1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           14
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       NRAS WILD-TYPE
  OTHER                                                                               7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     107
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             50
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                21
D2V4, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   16
  NRAS WILD-TYPE   12  173
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0             12
  YES           16            173
D2V5, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13    1
  NRAS WILD-TYPE  153    8
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            13            153
  YES            1              8

Clustering(3) Variable = HRAS MUTATION ANALYSIS
D3V1, continuous
D3V2, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7    3
  HRAS WILD-TYPE  142   49
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            7            142
  MALE              3             49
D3V3, multiclass
                                                                        clus
vv                                                                       HRAS MUTATED
  OTHER                                                                             1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     0
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       HRAS WILD-TYPE
  OTHER                                                                               7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     108
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             55
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                21
D3V4, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   10
  HRAS WILD-TYPE   12  179
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             0             12
  YES           10            179
D3V5, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     10    0
  HRAS WILD-TYPE  156    9
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            10            156
  YES            0              9

Clustering(4) Variable = EIF1AX MUTATION ANALYSIS
D4V1, continuous
D4V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      1    2
  EIF1AX WILD-TYPE  148   50
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              1              148
  MALE                2               50
D4V3, multiclass
                                                                        clus
vv                                                                       EIF1AX MUTATED
  OTHER                                                                               1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       0
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       EIF1AX WILD-TYPE
  OTHER                                                                                 7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       108
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               62
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  21
D4V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    3
  EIF1AX WILD-TYPE   12  186
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               0               12
  YES              3              186
D4V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    0
  EIF1AX WILD-TYPE  163    9
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               3              163
  YES              0                9

Clustering(5) Variable = EMG1 MUTATION ANALYSIS
D5V1, continuous
D5V2, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  145   52
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            4            145
  MALE              0             52
D5V3, multiclass
                                                                        clus
vv                                                                       EMG1 MUTATED
  OTHER                                                                             0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       EMG1 WILD-TYPE
  OTHER                                                                               8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             63
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                21
D5V4, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    4
  EMG1 WILD-TYPE   12  185
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             0             12
  YES            4            185
D5V5, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  162    9
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             4            162
  YES            0              9

Clustering(6) Variable = TG MUTATION ANALYSIS
D6V1, continuous
D6V2, binary
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      7    2
  TG WILD-TYPE  142   50
        clus
vv       TG MUTATED TG WILD-TYPE
  FEMALE          7          142
  MALE            2           50
D6V3, multiclass
                                                                        clus
vv                                                                       TG MUTATED
  OTHER                                                                           1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)          4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)             3
                                                                        clus
vv                                                                       TG WILD-TYPE
  OTHER                                                                             7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   107
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           60
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              18
D6V4, binary
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      0    9
  TG WILD-TYPE   12  180
     clus
vv    TG MUTATED TG WILD-TYPE
  NO           0           12
  YES          9          180
D6V5, binary
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      8    0
  TG WILD-TYPE  158    9
     clus
vv    TG MUTATED TG WILD-TYPE
  NO           8          158
  YES          0            9

Clustering(7) Variable = ZNF845 MUTATION ANALYSIS
D7V1, continuous
D7V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF845 MUTATED      3    0
  ZNF845 WILD-TYPE  146   52
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  FEMALE              3              146
  MALE                0               52
D7V3, multiclass
                                                                        clus
vv                                                                       ZNF845 MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       ZNF845 WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  21
D7V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF845 MUTATED      0    3
  ZNF845 WILD-TYPE   12  186
     clus
vv    ZNF845 MUTATED ZNF845 WILD-TYPE
  NO               0               12
  YES              3              186
D7V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF845 MUTATED      2    0
  ZNF845 WILD-TYPE  164    9
     clus
vv    ZNF845 MUTATED ZNF845 WILD-TYPE
  NO               2              164
  YES              0                9

Clustering(8) Variable = PPM1D MUTATION ANALYSIS
D8V1, continuous
D8V2, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      4    1
  PPM1D WILD-TYPE  145   51
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  FEMALE             4             145
  MALE               1              51
D8V3, multiclass
                                                                        clus
vv                                                                       PPM1D MUTATED
  OTHER                                                                              0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       PPM1D WILD-TYPE
  OTHER                                                                                8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      104
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              63
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 21
D8V4, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    5
  PPM1D WILD-TYPE   12  184
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              0              12
  YES             5             184
D8V5, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      4    0
  PPM1D WILD-TYPE  162    9
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              4             162
  YES             0               9

Clustering(9) Variable = ZNF799 MUTATION ANALYSIS
D9V1, continuous
D9V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      2    1
  ZNF799 WILD-TYPE  147   51
        clus
vv       ZNF799 MUTATED ZNF799 WILD-TYPE
  FEMALE              2              147
  MALE                1               51
D9V3, multiclass
                                                                        clus
vv                                                                       ZNF799 MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       ZNF799 WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  21
D9V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      0    3
  ZNF799 WILD-TYPE   12  186
     clus
vv    ZNF799 MUTATED ZNF799 WILD-TYPE
  NO               0               12
  YES              3              186
D9V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      2    0
  ZNF799 WILD-TYPE  164    9
     clus
vv    ZNF799 MUTATED ZNF799 WILD-TYPE
  NO               2              164
  YES              0                9

Clustering(10) Variable = CCDC15 MUTATION ANALYSIS
D10V1, continuous
D10V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC15 MUTATED      4    1
  CCDC15 WILD-TYPE  145   51
        clus
vv       CCDC15 MUTATED CCDC15 WILD-TYPE
  FEMALE              4              145
  MALE                1               51
D10V3, multiclass
                                                                        clus
vv                                                                       CCDC15 MUTATED
  OTHER                                                                               1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       CCDC15 WILD-TYPE
  OTHER                                                                                 7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       104
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  21
D10V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC15 MUTATED      0    5
  CCDC15 WILD-TYPE   12  184
     clus
vv    CCDC15 MUTATED CCDC15 WILD-TYPE
  NO               0               12
  YES              5              184
D10V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC15 MUTATED      4    0
  CCDC15 WILD-TYPE  162    9
     clus
vv    CCDC15 MUTATED CCDC15 WILD-TYPE
  NO               4              162
  YES              0                9

Clustering(11) Variable = COL5A3 MUTATION ANALYSIS
D11V1, continuous
D11V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED      4    0
  COL5A3 WILD-TYPE  145   52
        clus
vv       COL5A3 MUTATED COL5A3 WILD-TYPE
  FEMALE              4              145
  MALE                0               52
D11V3, multiclass
                                                                        clus
vv                                                                       COL5A3 MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 1
                                                                        clus
vv                                                                       COL5A3 WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  20
D11V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED      0    4
  COL5A3 WILD-TYPE   12  185
     clus
vv    COL5A3 MUTATED COL5A3 WILD-TYPE
  NO               0               12
  YES              4              185
D11V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A3 MUTATED      3    0
  COL5A3 WILD-TYPE  163    9
     clus
vv    COL5A3 MUTATED COL5A3 WILD-TYPE
  NO               3              163
  YES              0                9

Clustering(12) Variable = ZFHX3 MUTATION ANALYSIS
D12V1, continuous
D12V2, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      4    0
  ZFHX3 WILD-TYPE  145   52
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  FEMALE             4             145
  MALE               0              52
D12V3, multiclass
                                                                        clus
vv                                                                       ZFHX3 MUTATED
  OTHER                                                                              0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                1
                                                                        clus
vv                                                                       ZFHX3 WILD-TYPE
  OTHER                                                                                8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 20
D12V4, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      1    3
  ZFHX3 WILD-TYPE   11  186
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO              1              11
  YES             3             186
D12V5, binary
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      4    0
  ZFHX3 WILD-TYPE  162    9
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO              4             162
  YES             0               9

Clustering(13) Variable = DNMT3A MUTATION ANALYSIS
D13V1, continuous
D13V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      3    1
  DNMT3A WILD-TYPE  146   51
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              3              146
  MALE                1               51
D13V3, multiclass
                                                                        clus
vv                                                                       DNMT3A MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 1
                                                                        clus
vv                                                                       DNMT3A WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       106
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               63
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  20
D13V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0    4
  DNMT3A WILD-TYPE   12  185
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               0               12
  YES              4              185
D13V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      3    1
  DNMT3A WILD-TYPE  163    8
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               3              163
  YES              1                8

Clustering(14) Variable = FAM155A MUTATION ANALYSIS
D14V1, continuous
D14V2, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155A MUTATED      2    1
  FAM155A WILD-TYPE  147   51
        clus
vv       FAM155A MUTATED FAM155A WILD-TYPE
  FEMALE               2               147
  MALE                 1                51
D14V3, multiclass
                                                                        clus
vv                                                                       FAM155A MUTATED
  OTHER                                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       FAM155A WILD-TYPE
  OTHER                                                                                  7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        106
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   21
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155A MUTATED      0    3
  FAM155A WILD-TYPE   12  186
     clus
vv    FAM155A MUTATED FAM155A WILD-TYPE
  NO                0                12
  YES               3               186
D14V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155A MUTATED      2    0
  FAM155A WILD-TYPE  164    9
     clus
vv    FAM155A MUTATED FAM155A WILD-TYPE
  NO                2               164
  YES               0                 9

Clustering(15) Variable = KRAS MUTATION ANALYSIS
D15V1, continuous
D15V2, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    0
  KRAS WILD-TYPE  146   52
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            3            146
  MALE              0             52
D15V3, multiclass
                                                                        clus
vv                                                                       KRAS MUTATED
  OTHER                                                                             0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     0
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       KRAS WILD-TYPE
  OTHER                                                                               8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     108
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             61
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                21
D15V4, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    3
  KRAS WILD-TYPE   12  186
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0             12
  YES            3            186
D15V5, binary
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    0
  KRAS WILD-TYPE  163    9
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             3            163
  YES            0              9

Clustering(16) Variable = R3HDM2 MUTATION ANALYSIS
D16V1, continuous
D16V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      2    1
  R3HDM2 WILD-TYPE  147   51
        clus
vv       R3HDM2 MUTATED R3HDM2 WILD-TYPE
  FEMALE              2              147
  MALE                1               51
D16V3, multiclass
                                                                        clus
vv                                                                       R3HDM2 MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       R3HDM2 WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       107
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               62
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  21
D16V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      0    3
  R3HDM2 WILD-TYPE   12  186
     clus
vv    R3HDM2 MUTATED R3HDM2 WILD-TYPE
  NO               0               12
  YES              3              186
D16V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      2    0
  R3HDM2 WILD-TYPE  164    9
     clus
vv    R3HDM2 MUTATED R3HDM2 WILD-TYPE
  NO               2              164
  YES              0                9

Clustering(17) Variable = ARID1B MUTATION ANALYSIS
D17V1, continuous
D17V2, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      4    1
  ARID1B WILD-TYPE  145   51
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE              4              145
  MALE                1               51
D17V3, multiclass
                                                                        clus
vv                                                                       ARID1B MUTATED
  OTHER                                                                               0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 2
                                                                        clus
vv                                                                       ARID1B WILD-TYPE
  OTHER                                                                                 8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       106
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               63
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  19
D17V4, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      0    5
  ARID1B WILD-TYPE   12  184
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO               0               12
  YES              5              184
D17V5, binary
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      4    0
  ARID1B WILD-TYPE  162    9
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO               4              162
  YES              0                9
                                      V1 
                                   "AGE" 
                                      V2 
                                "GENDER" 
                                      V3 
                     "HISTOLOGICAL.TYPE" 
                                      V4 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V5 
                     "RADIATIONEXPOSURE" 
> q(save="no")
