
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/4466072/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/DLBC-TP/4434572/DLBC-TP.clin.merged.picked.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/GDAC_clinicalDataPicker/DLBC-TP/4434572/DLBC-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/4466072/transformed.cor.cli.txt"

nPatients in clinical file=21, in cluster file=18, common to both=16
[1] "Reduce the number of clustering variables from 80 to 9."
[1]  9 16
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                13 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                13 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                12 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                13 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 12 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 12 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 13 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 13 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 11 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 11 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                13 
[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] "BATCHNUMBER"                           

Input Data has 15 rows and 16 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        1081          946          965          126          832          679 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
         139           NA         1581         1441           NA           NA 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
        3226         5980         3872         2254 
Variable 1:'AGE':	nDistinctValues=13,	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=13,	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=11,	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:'BATCH.NUMBER':	nDistinctValues=1,	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 16 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=13, 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   3 0
  1Q GAIN WILD-TYPE 9 4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 4 
$`1Q GAIN MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-GR-7353 
        4.57        51.98        74.10 

$`1Q 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-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       41.13        47.38       211.23        19.56       106.06       196.60 
TCGA-GR-7351 
      127.30 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.57              4.14 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            74.10            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            51.98             35.54 
[1] "4.6 - 74.1 (52.0)"  "4.1 - 211.2 (35.5)"
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
[1] "hr="     "2.6e+08"
D1V2, continuous
D1V3, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   1 2
  1Q GAIN WILD-TYPE 8 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    2
  1Q GAIN WILD-TYPE    8    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               1                 8
  MALE                 2                 5

Clustering(2) Variable = 3Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2               0 1
  3Q GAIN MUTATED   3 0
  3Q GAIN WILD-TYPE 9 4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 4 
$`3Q GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8047 TCGA-G8-6914 
       31.10         4.14       196.60 

$`3Q GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       35.54        31.73        27.35        22.32         4.57        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-7353 
       74.10 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             4.14              4.57 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           196.60            211.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            31.10             41.13 
[1] "4.1 - 196.6 (31.1)" "4.6 - 211.2 (41.1)"
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr="     "2.5e+08"
D2V2, continuous
D2V3, binary
                   cls
clus                0 1
  3Q GAIN MUTATED   2 1
  3Q GAIN WILD-TYPE 7 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    1
  3Q GAIN WILD-TYPE    7    6
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                 7
  MALE                 1                 6

Clustering(3) Variable = 7P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2               0 1
  7P GAIN MUTATED   4 0
  7P GAIN WILD-TYPE 8 4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 4 
$`7P GAIN MUTATED`
TCGA-FF-8042 TCGA-FM-8000 TCGA-G8-6914 TCGA-GR-7353 
       31.10         4.57       196.60        74.10 

$`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 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.57              4.14 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           196.60            211.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           52.600            38.335 
[1] "4.6 - 196.6 (52.6)" "4.1 - 211.2 (38.3)"
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
[1] "hr="     "7.6e+08"
D3V2, continuous
D3V3, binary
                   cls
clus                0 1
  7P GAIN MUTATED   2 2
  7P GAIN WILD-TYPE 7 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    2
  7P GAIN WILD-TYPE    7    5
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               2                 7
  MALE                 2                 5

Clustering(4) Variable = 7Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2               0 1
  7Q GAIN MUTATED   3 0
  7Q GAIN WILD-TYPE 9 4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 4 
$`7Q GAIN MUTATED`
TCGA-FF-8042 TCGA-FM-8000 TCGA-GR-7353 
       31.10         4.57        74.10 

$`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 
      127.30 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.57              4.14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            74.10            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            31.10             41.13 
[1] "4.6 - 74.1 (31.1)"  "4.1 - 211.2 (41.1)"
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
[1] "hr="     "2.2e+08"
D4V2, continuous
D4V3, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   2 1
  7Q GAIN WILD-TYPE 7 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    1
  7Q GAIN WILD-TYPE    7    6
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               2                 7
  MALE                 1                 6

Clustering(5) Variable = 11Q GAIN MUTATION ANALYSIS
D5V1, survival
                    sevent
clus2                0 1
  11Q GAIN MUTATED   4 0
  11Q GAIN WILD-TYPE 8 4
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 12 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  4 
$`11Q GAIN MUTATED`
TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-7353 
       35.54        31.73       127.30        74.10 

$`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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             31.73               4.14 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            127.30             211.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            54.820             36.115 
[1] "31.7 - 127.3 (54.8)" "4.1 - 211.2 (36.1)" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GR-7353 
  "11Q GAIN MUTATED" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GR-7353 
  "11Q GAIN MUTATED" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GR-7353 
  "11Q GAIN MUTATED" 
[1] "hr="   "8e+08"
D5V2, continuous
D5V3, binary
                    cls
clus                 0 1
  11Q GAIN MUTATED   3 1
  11Q GAIN WILD-TYPE 6 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    1
  11Q GAIN WILD-TYPE    6    6
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                  6
  MALE                  1                  6

Clustering(6) Variable = 18P GAIN MUTATION ANALYSIS
D6V1, survival
                    sevent
clus2                0 1
  18P GAIN MUTATED   3 0
  18P GAIN WILD-TYPE 9 4
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  4 
$`18P GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 
       31.10        31.73       196.60 

$`18P GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       35.54         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-GR-7351 
       51.98        47.38       211.23        19.56       106.06       127.30 
TCGA-GR-7353 
       74.10 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             31.10               4.14 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            196.60             211.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             31.73              41.13 
[1] "31.1 - 196.6 (31.7)" "4.1 - 211.2 (41.1)" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18P GAIN WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18P GAIN WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+08"
D6V2, continuous
D6V3, binary
                    cls
clus                 0 1
  18P GAIN MUTATED   2 1
  18P GAIN WILD-TYPE 7 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE    7    6
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                  7
  MALE                  1                  6

Clustering(7) Variable = 18Q GAIN MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                0 1
  18Q GAIN MUTATED   3 0
  18Q GAIN WILD-TYPE 9 4
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  4 
$`18Q GAIN MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-G8-6914 
       31.10        31.73       196.60 

$`18Q GAIN WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       35.54         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-GR-7351 
       51.98        47.38       211.23        19.56       106.06       127.30 
TCGA-GR-7353 
       74.10 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             31.10               4.14 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            196.60             211.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             31.73              41.13 
[1] "31.1 - 196.6 (31.7)" "4.1 - 211.2 (41.1)" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18Q GAIN WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18Q GAIN WILD-TYPE" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GR-7353 
"18Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+08"
D7V2, continuous
D7V3, binary
                    cls
clus                 0 1
  18Q GAIN MUTATED   2 1
  18Q GAIN WILD-TYPE 7 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE    7    6
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                2                  7
  MALE                  1                  6

Clustering(8) Variable = 21Q GAIN MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                0 1
  21Q GAIN MUTATED   4 1
  21Q GAIN WILD-TYPE 8 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 11 
  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-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-G8-6914 
       51.98        47.38       211.23        19.56       196.60 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             31.73               4.14 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            127.30             211.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              74.1               31.1 
[1] "31.7 - 127.3 (74.1)" "4.1 - 211.2 (31.1)" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-GR-7353 
  "21Q GAIN MUTATED" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-GR-7353 
  "21Q GAIN MUTATED" 
        TCGA-FF-8041         TCGA-FF-8042         TCGA-FF-8043 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FF-8047         TCGA-FF-8061         TCGA-FF-8062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6325 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-G8-6907 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G8-6909         TCGA-G8-6914         TCGA-GR-7351 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-GR-7353 
  "21Q GAIN MUTATED" 
[1] "hr=" "1.4"
D8V2, continuous
D8V3, binary
                    cls
clus                 0 1
  21Q GAIN MUTATED   3 2
  21Q GAIN WILD-TYPE 6 5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE    6    5
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                  6
  MALE                  2                  5

Clustering(9) Variable = XQ LOSS MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 10  3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                13 
  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-FF-8041 TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       35.54        31.10        27.35        22.32         4.57        41.13 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       106.06       196.60       127.30 
TCGA-GR-7353 
       74.10 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.14              4.57 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.73            211.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.56             47.38 
[1] "4.1 - 31.7 (19.6)"  "4.6 - 211.2 (47.4)"
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8047 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FM-8000        TCGA-G8-6324 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6907 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-G8-6909        TCGA-G8-6914        TCGA-GR-7351        TCGA-GR-7353 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr="     "3.6e+09"
D9V2, continuous
D9V3, binary
                   cls
clus                0 1
  XQ LOSS MUTATED   3 0
  XQ LOSS WILD-TYPE 6 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE    6    7
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                 6
  MALE                 0                 7
> q(save="no")
