
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/10441/12/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/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/6158323/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/6154398/DLBC-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=DLBC-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=DLBC-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/DLBC-TP/6154398/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/6158323/transformed.cor.cli.txt"

nPatients in clinical file=21, in cluster file=28, common to both=21
[1] "Reduce the number of clustering variables from 80 to 17."
[1] 17 21
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                17 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                17 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                18 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                18 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                17 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                14 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                14 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                15 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                15 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 18 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 18 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 14 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 14 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 18 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 18 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 18 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 18 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 18 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 18 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 18 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 18 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 17 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 17 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 16 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 18 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 18 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                18 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                18 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[12] "RADIATIONTHERAPY"                      
[13] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "GLEASON_SCORE"                         
[16] "PSA_VALUE"                             
[17] "DAYS_TO_PSA"                           
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 21 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
          62         1081          946          965          126          832 
TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
         679          139           NA         1581         1441           NA 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
          NA         3226         5980         3872         2254          812 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
         751          911         1408 
Variable 1:'AGE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 21 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=17, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    4  0
  1Q GAIN WILD-TYPE 13  4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                17 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 4 
$`1Q GAIN MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-GR-7353 TCGA-GR-A4D9 
        4.57        51.98        74.10        46.29 

$`1Q GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
        2.04        35.54        31.10        31.73         4.14        27.35 
TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       22.32        41.13        47.38       211.23        19.56       106.06 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       127.30        26.70        24.69        29.95 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.57              2.04 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            74.10            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           49.135            31.100 
[1] "4.6 - 74.1 (49.1)"  "2.0 - 211.2 (31.1)"
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-A4D9 
  "1Q GAIN MUTATED" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-A4D9 
  "1Q GAIN MUTATED" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GR-A4D9 
  "1Q GAIN MUTATED" 
[1] "hr="     "3.1e+08"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 11  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   11    6
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               2                11
  MALE                 2                 6

Clustering(2) Variable = 3P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  0
  3P GAIN WILD-TYPE 14  4
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                18 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 4 
$`3P GAIN MUTATED`
TCGA-FF-8042 TCGA-G8-6914 TCGA-GR-A4D6 
       31.10       196.60        29.95 

$`3P GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        2.04        35.54        31.73         4.14        27.35        22.32 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.13        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      106.06       127.30        74.10        26.70        24.69        46.29 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            29.95              2.04 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           196.60            211.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           31.100            33.635 
[1] "29.9 - 196.6 (31.1)" "2.0 - 211.2 (33.6)" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GR-A4D9 
"3P GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GR-A4D9 
"3P GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GR-A4D9 
"3P GAIN WILD-TYPE" 
[1] "hr="     "2.5e+08"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 11  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    1
  3P GAIN WILD-TYPE   11    7
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                11
  MALE                 1                 7

Clustering(3) Variable = 3Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  0
  3Q GAIN WILD-TYPE 13  4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 4 
$`3Q GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8047 TCGA-G8-6914 TCGA-GR-A4D6 
       31.10         4.14       196.60        29.95 

$`3Q GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        35.54        31.73        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      127.30        74.10        26.70        24.69        46.29 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             4.14              2.04 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           196.60            211.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           30.525            35.540 
[1] "4.1 - 196.6 (30.5)" "2.0 - 211.2 (35.5)"
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"3Q GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"3Q GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"3Q GAIN WILD-TYPE" 
[1] "hr="     "2.5e+08"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  1
  3Q GAIN WILD-TYPE 10  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    1
  3Q GAIN WILD-TYPE   10    7
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                10
  MALE                 1                 7

Clustering(4) Variable = 7P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    7  0
  7P GAIN WILD-TYPE 10  4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                14 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 4 
$`7P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FM-8000 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 
        2.04        31.10         4.57       196.60        74.10        26.70 
TCGA-GR-A4D6 
       29.95 

$`7P GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 
       35.54        31.73         4.14        27.35        22.32        41.13 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 
       51.98        47.38       211.23        19.56       106.06       127.30 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       24.69        46.29 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             2.04              4.14 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           196.60            211.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           29.950            38.335 
[1] "2.0 - 196.6 (29.9)" "4.1 - 211.2 (38.3)"
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GR-A4D9 
"7P GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GR-A4D9 
"7P GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GR-A4D9 
"7P GAIN WILD-TYPE" 
[1] "hr="     "7.8e+08"
D4V2, continuous
D4V3, binary
                   cls
clus                0 1
  7P GAIN MUTATED   4 3
  7P GAIN WILD-TYPE 9 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    3
  7P GAIN WILD-TYPE    9    5
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               4                 9
  MALE                 3                 5

Clustering(5) Variable = 7Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    6  0
  7Q GAIN WILD-TYPE 11  4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                15 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 4 
$`7Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
        2.04        31.10         4.57        74.10        26.70        29.95 

$`7Q GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 
       35.54        31.73         4.14        27.35        22.32        41.13 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.06       196.60 
TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
      127.30        24.69        46.29 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             2.04              4.14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            74.10            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           28.325            41.130 
[1] "2.0 - 74.1 (28.3)"  "4.1 - 211.2 (41.1)"
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"7Q GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"7Q GAIN WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GR-A4D9 
"7Q GAIN WILD-TYPE" 
[1] "hr="     "2.5e+08"
D5V2, continuous
D5V3, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   4 2
  7Q GAIN WILD-TYPE 9 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    2
  7Q GAIN WILD-TYPE    9    6
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               4                 9
  MALE                 2                 6

Clustering(6) Variable = 11P GAIN MUTATION ANALYSIS
D6V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 14  4
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 18 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  4 
$`11P GAIN MUTATED`
TCGA-FF-8043 TCGA-GR-A4D5 TCGA-GR-A4D9 
       31.73        24.69        46.29 

$`11P GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        2.04        35.54        31.10         4.14        27.35        22.32 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.13        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      106.06       196.60       127.30        74.10        26.70        29.95 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             24.69               2.04 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             46.29             211.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             31.73              33.32 
[1] "24.7 - 46.3 (31.7)" "2.0 - 211.2 (33.3)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
[1] "hr="     "2.3e+08"
D6V2, continuous
D6V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 10  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   10    8
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 10
  MALE                  0                  8

Clustering(7) Variable = 11Q GAIN MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    7  0
  11Q GAIN WILD-TYPE 10  4
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 14 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  4 
$`11Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 
        2.04        35.54        31.73       127.30        74.10        24.69 
TCGA-GR-A4D9 
       46.29 

$`11Q GAIN WILD-TYPE`
TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       31.10         4.14        27.35        22.32         4.57        41.13 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.06       196.60 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.70        29.95 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2.04               4.14 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            127.30             211.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            35.540             30.525 
[1] "2.0 - 127.3 (35.5)" "4.1 - 211.2 (30.5)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
[1] "hr="   "9e+08"
D7V2, continuous
D7V3, binary
                    cls
clus                 0 1
  11Q GAIN MUTATED   5 2
  11Q GAIN WILD-TYPE 8 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    2
  11Q GAIN WILD-TYPE    8    6
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                  8
  MALE                  2                  6

Clustering(8) Variable = 12P GAIN MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    3  0
  12P GAIN WILD-TYPE 14  4
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 18 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  4 
$`12P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-GR-A4D5 
        2.04        35.54        24.69 

$`12P GAIN WILD-TYPE`
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       31.10        31.73         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       127.30        74.10        26.70        29.95        46.29 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2.04               4.14 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             35.54             211.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             24.69              36.43 
[1] "2.0 - 35.5 (24.7)"  "4.1 - 211.2 (36.4)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr="     "7.9e+07"
D8V2, continuous
D8V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  1
  12P GAIN WILD-TYPE 11  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    1
  12P GAIN WILD-TYPE   11    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 11
  MALE                  1                  7

Clustering(9) Variable = 12Q GAIN MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 14  4
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 18 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  4 
$`12Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-GR-A4D5 
        2.04        35.54        24.69 

$`12Q GAIN WILD-TYPE`
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       31.10        31.73         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       127.30        74.10        26.70        29.95        46.29 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              2.04               4.14 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             35.54             211.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             24.69              36.43 
[1] "2.0 - 35.5 (24.7)"  "4.1 - 211.2 (36.4)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr="     "7.9e+07"
D9V2, continuous
D9V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  1
  12Q GAIN WILD-TYPE 11  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    1
  12Q GAIN WILD-TYPE   11    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 11
  MALE                  1                  7

Clustering(10) Variable = 16P GAIN MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    3  0
  16P GAIN WILD-TYPE 14  4
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 18 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  4 
$`16P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-GR-A4D4 
        2.04         4.57        26.70 

$`16P GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73         4.14        27.35        22.32 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       127.30        74.10        24.69        29.95        46.29 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.04               4.14 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             26.70             211.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             4.570             38.335 
[1] "2.0 - 26.7 (4.6)"   "4.1 - 211.2 (38.3)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D10V2, continuous
D10V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  1
  16P GAIN WILD-TYPE 11  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    1
  16P GAIN WILD-TYPE   11    7
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                2                 11
  MALE                  1                  7

Clustering(11) Variable = 16Q GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2  1
  16Q GAIN WILD-TYPE 15  3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 18 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  3 
$`16Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6909 
        2.04         4.57       106.06 

$`16Q GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73         4.14        27.35        22.32 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 
       41.13        51.98        47.38       211.23        19.56       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      127.30        74.10        26.70        24.69        29.95        46.29 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.04               4.14 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            106.06             211.23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             4.570             33.635 
[1] "2.0 - 106.1 (4.6)"  "4.1 - 211.2 (33.6)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "3.4"
D11V2, continuous
D11V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  2
  16Q GAIN WILD-TYPE 12  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    2
  16Q GAIN WILD-TYPE   12    6
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 12
  MALE                  2                  6

Clustering(12) Variable = 18P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    4  0
  18P GAIN WILD-TYPE 13  4
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  4 
$`18P GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 TCGA-GR-A4D6 
       31.10        31.73       196.60        29.95 

$`18P GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        35.54         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      127.30        74.10        26.70        24.69        46.29 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             29.95               2.04 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            196.60             211.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            31.415             35.540 
[1] "29.9 - 196.6 (31.4)" "2.0 - 211.2 (35.5)" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+08"
D12V2, continuous
D12V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  1
  18P GAIN WILD-TYPE 10  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    1
  18P GAIN WILD-TYPE   10    7
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 10
  MALE                  1                  7

Clustering(13) Variable = 18Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 13  4
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  4 
$`18Q GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 TCGA-GR-A4D6 
       31.10        31.73       196.60        29.95 

$`18Q GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        35.54         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      127.30        74.10        26.70        24.69        46.29 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             29.95               2.04 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            196.60             211.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            31.415             35.540 
[1] "29.9 - 196.6 (31.4)" "2.0 - 211.2 (35.5)" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+08"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  1
  18Q GAIN WILD-TYPE 10  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    1
  18Q GAIN WILD-TYPE   10    7
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 10
  MALE                  1                  7

Clustering(14) Variable = 21Q GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    4  1
  21Q GAIN WILD-TYPE 13  3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  3 
$`21Q GAIN MUTATED`
TCGA-FF-8041 TCGA-FF-8043 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       35.54        31.73       106.06       127.30        74.10 

$`21Q GAIN WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        31.10         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 
       41.13        51.98        47.38       211.23        19.56       196.60 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             31.73               2.04 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            127.30             211.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             74.10              28.65 
[1] "31.7 - 127.3 (74.1)" "2.0 - 211.2 (28.6)" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  2
  21Q GAIN WILD-TYPE 10  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE   10    6
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 10
  MALE                  2                  6

Clustering(15) Variable = 15Q LOSS MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    4  0
  15Q LOSS WILD-TYPE 13  4
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  4 
$`15Q LOSS MUTATED`
TCGA-FF-8043 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       31.73        74.10        26.70        29.95 

$`15Q LOSS WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        2.04        35.54        31.10         4.14        27.35        22.32 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.13        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
      106.06       196.60       127.30        24.69        46.29 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             26.70               2.04 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             74.10             211.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             30.84              35.54 
[1] "26.7 - 74.1 (30.8)" "2.0 - 211.2 (35.5)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  1
  15Q LOSS WILD-TYPE 10  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    1
  15Q LOSS WILD-TYPE   10    7
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                 10
  MALE                  1                  7

Clustering(16) Variable = 16Q LOSS MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    3  0
  16Q LOSS WILD-TYPE 14  4
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 18 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  4 
$`16Q LOSS MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
       31.73         4.14        26.70 

$`16Q LOSS WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        35.54        31.10        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.13        51.98        47.38       211.23        19.56       106.06 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       127.30        74.10        24.69        29.95        46.29 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              4.14               2.04 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             31.73             211.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            26.700             38.335 
[1] "4.1 - 31.7 (26.7)"  "2.0 - 211.2 (38.3)"
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FA-A4XK         TCGA-FF-8041         TCGA-FF-8042 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8043         TCGA-FF-8047         TCGA-FF-8061 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FM-8000         TCGA-G8-6324 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6325         TCGA-G8-6326         TCGA-G8-6906 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6907         TCGA-G8-6909         TCGA-G8-6914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-7353         TCGA-GR-A4D4 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GR-A4D5         TCGA-GR-A4D6         TCGA-GR-A4D9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  0
  16Q LOSS WILD-TYPE 10  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    0
  16Q LOSS WILD-TYPE   10    8
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 10
  MALE                  0                  8

Clustering(17) Variable = XQ LOSS MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 15  3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                18 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 3 
$`XQ LOSS MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6907 
       31.73         4.14        19.56 

$`XQ LOSS WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
        2.04        35.54        31.10        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 
       41.13        51.98        47.38       211.23       106.06       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      127.30        74.10        26.70        24.69        29.95        46.29 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.14              2.04 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.73            211.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           19.560            38.335 
[1] "4.1 - 31.7 (19.6)"  "2.0 - 211.2 (38.3)"
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-A4D9 
"XQ LOSS WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-A4D9 
"XQ LOSS WILD-TYPE" 
       TCGA-FA-A4XK        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6907        TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-7353        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-A4D9 
"XQ LOSS WILD-TYPE" 
[1] "hr="     "3.6e+09"
D17V2, continuous
D17V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  0
  XQ LOSS WILD-TYPE 10  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE   10    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                10
  MALE                 0                 8
> q(save="no")
