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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/6068695/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/6154438/KIRP-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/6154438/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/6068695/transformed.cor.cli.txt"

nPatients in clinical file=139, in cluster file=112, common to both=109
[1] "Reduce the number of clustering variables from 2 to 1."
[1]   1 109
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            7           102 
  NF2 MUTATED NF2 WILD-TYPE 
            7           102 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "GLEASON_SCORE"                         
[21] "PSA_VALUE"                             
[22] "DAYS_TO_PSA"                           
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 109 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
         582           27           NA            7           49          140 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-AL-3466 
           1            2           22            3           NA           NA 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1778         1636          922          763         1357          595 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        1029          307          929         1049          379         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         856          803          626           14           33          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         804          671         2638          585           NA         1938 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
          NA           NA         1454           NA         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
         921          792          771          403           NA          232 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
          29          364           NA           84         3759           NA 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2948         2839           NA         1864         1532         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
         799          612           NA          232          213          217 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
         115          353          414         3950         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         418          114          445           92         2428         2459 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          NA         1856         1669         1040          578          757 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1574         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          445          785         5924          393          112 
TCGA-GL-8500 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-IZ-8195 TCGA-IZ-8196 
         235           NA           NA           NA           33          123 
TCGA-J7-6720 
          NA 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 20:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE" "HISTOLOGICAL.TYPE"          
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 109 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
61 13 34  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   61    13    35 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
61 13 34  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   61    13    35 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
22 11  4 
[1] "table(vv)"
vv
N0 N1 N2 
22 11  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
22 11  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
22 11  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NF2 MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  NF2 MUTATED    6  1
  NF2 WILD-TYPE 81 14
  NF2 MUTATED NF2 WILD-TYPE 
            7            95 
  NF2 MUTATED NF2 WILD-TYPE 
            1            14 
$`NF2 MUTATED`
TCGA-A4-8098 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 TCGA-EV-5902 TCGA-G7-6797 
        4.60        86.73         8.84         2.76        19.00        25.15 
TCGA-GL-7966 
        3.68 

$`NF2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21         0.69        15.95         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8516 
        0.89         0.23         1.61         0.03         0.07         0.72 
TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
        0.10         9.63        58.45        53.79        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       44.61        19.56        33.83        10.09        30.54        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.14        26.40        20.58         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 TCGA-BQ-5878 
        1.08        15.12        26.43        22.06        19.23        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       61.02        54.87        34.19        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        39.25        34.82        14.63        25.81 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-IZ-8195 TCGA-IZ-8196 
      194.76        12.92         7.73         1.08         4.04 

  NF2 MUTATED NF2 WILD-TYPE 
         2.76          0.03 
  NF2 MUTATED NF2 WILD-TYPE 
        86.73        194.76 
  NF2 MUTATED NF2 WILD-TYPE 
         8.84         22.06 
[1] "2.8 - 86.7 (8.8)"   "0.0 - 194.8 (22.1)"
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-IZ-8195    TCGA-IZ-8196 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-IZ-8195    TCGA-IZ-8196 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-IZ-8195    TCGA-IZ-8196 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
[1] "hr=" "1.5"
D1V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         3        2
  NF2 WILD-TYPE      54        8        23        7
D1V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2            54
  STAGE II            0             8
  STAGE III           3            23
  STAGE IV            2             7
               vv
clus            T1 T2 T3+T4
  NF2 MUTATED    3  0     4
  NF2 WILD-TYPE 58 13    31
D1V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              3            58
  T2              0            13
  T3+T4           4            31
               vv
clus            N0 N1 N2
  NF2 MUTATED    0  3  0
  NF2 WILD-TYPE 22  8  4
D1V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           0            22
  N1           3             8
  N2           0             4
               vv
clus            M0 M1 MX
  NF2 MUTATED    2  2  3
  NF2 WILD-TYPE 52  3 39
D1V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  M0           2            52
  M1           2             3
  MX           3            39
D1V7, binary
               cls
clus             0  1
  NF2 MUTATED    2  5
  NF2 WILD-TYPE 32 70
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    5
  NF2 WILD-TYPE   32   70
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           2            32
  MALE             5            70
D1V8, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            23 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8518 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-8630    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7842    TCGA-EV-5901    TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6796    TCGA-G7-7501    TCGA-G7-7502 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
D1V9, binary
               cls
clus             0  1
  NF2 MUTATED    1  6
  NF2 WILD-TYPE  5 97
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    6
  NF2 WILD-TYPE    5   97
                                       clus
vv                                      NF2 MUTATED NF2 WILD-TYPE
  KIDNEY CLEAR CELL RENAL CARCINOMA               1             5
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           6            97
> q(save="no")
