
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/8278307/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/8142765/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/8142765/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/8278307/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 26 to 21."
[1] 21 21
[1] "AMP PEAK 1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           7                           14 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           7                           14 
[1] "AMP PEAK 2(2P15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         14 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         14 
[1] "AMP PEAK 3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           5                           16 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           5                           16 
[1] "AMP PEAK 4(8Q24.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            5                            16 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            5                            16 
[1] "AMP PEAK 5(12Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             17 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             17 
[1] "AMP PEAK 6(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            16 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            16 
[1] "AMP PEAK 7(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           4                           17 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           4                           17 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            4                            17 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            4                            17 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          4                          17 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          4                          17 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            4                            17 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            4                            17 
[1] "DEL PEAK  5(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            6                            15 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            6                            15 
[1] "DEL PEAK  6(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            16 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            16 
[1] "DEL PEAK 10(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            14 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            14 
[1] "DEL PEAK 11(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              17 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              17 
[1] "DEL PEAK 12(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             18 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             18 
[1] "DEL PEAK 13(13Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             17 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             17 
[1] "DEL PEAK 14(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             6                             15 
[1] "DEL PEAK 15(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             6                             15 
[1] "DEL PEAK 16(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              3                              18 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              3                              18 
[1] "DEL PEAK 17(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             3                             18 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             3                             18 
[1] "DEL PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             3                             18 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) 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         3227         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 = AMP PEAK 1(1Q31.1) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 1(1Q31.1) MUTATED    7  0
  AMP PEAK 1(1Q31.1) WILD-TYPE 10  4
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           7                           14 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           0                            4 
$`AMP PEAK 1(1Q31.1) MUTATED`
TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D6 
        4.14         4.57        51.98       196.60        74.10        29.95 
TCGA-GR-A4D9 
       46.29 

$`AMP PEAK 1(1Q31.1) WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 
        2.04        35.54        31.10        31.73        27.35        22.32 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 
       41.16        47.38       211.23        19.56       106.09       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 
       26.70        24.69 

  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                        4.14                         2.04 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                      196.60                       211.23 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                      46.290                       31.415 
[1] "4.1 - 196.6 (46.3)" "2.0 - 211.2 (31.4)"
                  TCGA-FA-A4XK                   TCGA-FF-8041 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-GR-A4D9 
  "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-GR-A4D9 
  "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 1(1Q31.1) WILD-TYPE" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
  "AMP PEAK 1(1Q31.1) MUTATED" "AMP PEAK 1(1Q31.1) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 1(1Q31.1) WILD-TYPE"   "AMP PEAK 1(1Q31.1) MUTATED" 
                  TCGA-GR-A4D9 
  "AMP PEAK 1(1Q31.1) MUTATED" 
[1] "hr="   "1e+09"
D1V2, continuous
D1V3, binary
                              cls
clus                           0 1
  AMP PEAK 1(1Q31.1) MUTATED   4 3
  AMP PEAK 1(1Q31.1) WILD-TYPE 9 5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.1) MUTATED      4    3
  AMP PEAK 1(1Q31.1) WILD-TYPE    9    5
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  FEMALE                          4                            9
  MALE                            3                            5

Clustering(2) Variable = AMP PEAK 2(2P15) MUTATION ANALYSIS
D2V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 2(2P15) MUTATED    5  2
  AMP PEAK 2(2P15) WILD-TYPE 12  2
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         14 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         2                          2 
$`AMP PEAK 2(2P15) MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 TCGA-FM-8000 TCGA-G8-6907 
        2.04        35.54        31.73        27.35         4.57        19.56 
TCGA-G8-6909 
      106.09 

$`AMP PEAK 2(2P15) WILD-TYPE`
TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       31.10         4.14        22.32        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      211.23       196.60       127.30        74.10        26.70        24.69 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       29.95        46.29 

  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                      2.04                       4.14 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                    106.09                     211.23 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                    27.350                     43.725 
[1] "2.0 - 106.1 (27.4)" "4.1 - 211.2 (43.7)"
                TCGA-FA-A4XK                 TCGA-FF-8041 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8042                 TCGA-FF-8043 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8047                 TCGA-FF-8061 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8062                 TCGA-FM-8000 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6324                 TCGA-G8-6325 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6326                 TCGA-G8-6906 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6907                 TCGA-G8-6909 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6914                 TCGA-GR-7351 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-7353                 TCGA-GR-A4D4 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D5                 TCGA-GR-A4D6 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D9 
"AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-FA-A4XK                 TCGA-FF-8041 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8042                 TCGA-FF-8043 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8047                 TCGA-FF-8061 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8062                 TCGA-FM-8000 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6324                 TCGA-G8-6325 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6326                 TCGA-G8-6906 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6907                 TCGA-G8-6909 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6914                 TCGA-GR-7351 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-7353                 TCGA-GR-A4D4 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D5                 TCGA-GR-A4D6 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D9 
"AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-FA-A4XK                 TCGA-FF-8041 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8042                 TCGA-FF-8043 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8047                 TCGA-FF-8061 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-FF-8062                 TCGA-FM-8000 
"AMP PEAK 2(2P15) WILD-TYPE"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6324                 TCGA-G8-6325 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6326                 TCGA-G8-6906 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-G8-6907                 TCGA-G8-6909 
  "AMP PEAK 2(2P15) MUTATED"   "AMP PEAK 2(2P15) MUTATED" 
                TCGA-G8-6914                 TCGA-GR-7351 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-7353                 TCGA-GR-A4D4 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D5                 TCGA-GR-A4D6 
"AMP PEAK 2(2P15) WILD-TYPE" "AMP PEAK 2(2P15) WILD-TYPE" 
                TCGA-GR-A4D9 
"AMP PEAK 2(2P15) WILD-TYPE" 
[1] "hr=" "8.2"
D2V2, continuous
D2V3, binary
                            cls
clus                         0 1
  AMP PEAK 2(2P15) MUTATED   4 3
  AMP PEAK 2(2P15) WILD-TYPE 9 5
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(2P15) MUTATED      4    3
  AMP PEAK 2(2P15) WILD-TYPE    9    5
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  FEMALE                        4                          9
  MALE                          3                          5

Clustering(3) Variable = AMP PEAK 3(3Q27.3) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 3(3Q27.3) MUTATED    5  0
  AMP PEAK 3(3Q27.3) WILD-TYPE 12  4
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           5                           16 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           0                            4 
$`AMP PEAK 3(3Q27.3) MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D6 
        2.04        31.10       196.60        26.70        29.95 

$`AMP PEAK 3(3Q27.3) WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       35.54        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 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D9 
      127.30        74.10        24.69        46.29 

  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                        2.04                         4.14 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                      196.60                       211.23 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                       29.95                        38.35 
[1] "2.0 - 196.6 (29.9)" "4.1 - 211.2 (38.3)"
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D9 
"AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D9 
"AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 3(3Q27.3) WILD-TYPE" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
  "AMP PEAK 3(3Q27.3) MUTATED" "AMP PEAK 3(3Q27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 3(3Q27.3) WILD-TYPE"   "AMP PEAK 3(3Q27.3) MUTATED" 
                  TCGA-GR-A4D9 
"AMP PEAK 3(3Q27.3) WILD-TYPE" 
[1] "hr="     "2.6e+08"
D3V2, continuous
D3V3, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.3) MUTATED    3  2
  AMP PEAK 3(3Q27.3) WILD-TYPE 10  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.3) MUTATED      3    2
  AMP PEAK 3(3Q27.3) WILD-TYPE   10    6
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  FEMALE                          3                           10
  MALE                            2                            6

Clustering(4) Variable = AMP PEAK 4(8Q24.12) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 4(8Q24.12) MUTATED    5  0
  AMP PEAK 4(8Q24.12) WILD-TYPE 12  4
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            5                            16 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            0                             4 
$`AMP PEAK 4(8Q24.12) MUTATED`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-GR-7353 
       35.54        31.10        31.73        27.35        74.10 

$`AMP PEAK 4(8Q24.12) WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8047 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        2.04         4.14        22.32         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                        27.35                          2.04 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                        74.10                        211.23 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                       31.730                        35.555 
[1] "27.4 - 74.1 (31.7)" "2.0 - 211.2 (35.6)"
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "AMP PEAK 4(8Q24.12) MUTATED"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "AMP PEAK 4(8Q24.12) MUTATED" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "AMP PEAK 4(8Q24.12) MUTATED"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "AMP PEAK 4(8Q24.12) MUTATED" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "AMP PEAK 4(8Q24.12) MUTATED"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 4(8Q24.12) WILD-TYPE"   "AMP PEAK 4(8Q24.12) MUTATED" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "AMP PEAK 4(8Q24.12) MUTATED" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 4(8Q24.12) WILD-TYPE" "AMP PEAK 4(8Q24.12) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 4(8Q24.12) WILD-TYPE" 
[1] "hr="     "2.7e+08"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK 4(8Q24.12) MUTATED    3  2
  AMP PEAK 4(8Q24.12) WILD-TYPE 10  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(8Q24.12) MUTATED      3    2
  AMP PEAK 4(8Q24.12) WILD-TYPE   10    6
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  FEMALE                           3                            10
  MALE                             2                             6

Clustering(5) Variable = AMP PEAK 5(12Q13.12) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 5(12Q13.12) MUTATED    4  0
  AMP PEAK 5(12Q13.12) WILD-TYPE 13  4
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             17 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             0                              4 
$`AMP PEAK 5(12Q13.12) MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-A4D5 
        2.04        35.54        31.73        24.69 

$`AMP PEAK 5(12Q13.12) 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        41.16 
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       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      127.30        74.10        26.70        29.95        46.29 

  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                          2.04                           4.14 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                         35.54                         211.23 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                         28.21                          41.16 
[1] "2.0 - 35.5 (28.2)"  "4.1 - 211.2 (41.2)"
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "AMP PEAK 5(12Q13.12) MUTATED"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"AMP PEAK 5(12Q13.12) WILD-TYPE"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
  "AMP PEAK 5(12Q13.12) MUTATED" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D9 
"AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "AMP PEAK 5(12Q13.12) MUTATED"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"AMP PEAK 5(12Q13.12) WILD-TYPE"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
  "AMP PEAK 5(12Q13.12) MUTATED" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D9 
"AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "AMP PEAK 5(12Q13.12) MUTATED"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"AMP PEAK 5(12Q13.12) WILD-TYPE"   "AMP PEAK 5(12Q13.12) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"AMP PEAK 5(12Q13.12) WILD-TYPE" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
  "AMP PEAK 5(12Q13.12) MUTATED" "AMP PEAK 5(12Q13.12) WILD-TYPE" 
                    TCGA-GR-A4D9 
"AMP PEAK 5(12Q13.12) WILD-TYPE" 
[1] "hr="     "8.8e+07"
D5V2, continuous
D5V3, binary
                                cls
clus                              0  1
  AMP PEAK 5(12Q13.12) MUTATED    3  1
  AMP PEAK 5(12Q13.12) WILD-TYPE 10  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(12Q13.12) MUTATED      3    1
  AMP PEAK 5(12Q13.12) WILD-TYPE   10    7
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  FEMALE                            3                             10
  MALE                              1                              7

Clustering(6) Variable = AMP PEAK 6(16P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 6(16P11.2) MUTATED    4  1
  AMP PEAK 6(16P11.2) WILD-TYPE 13  3
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            16 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            1                             3 
$`AMP PEAK 6(16P11.2) MUTATED`
TCGA-FA-A4XK TCGA-FF-8043 TCGA-FM-8000 TCGA-G8-6909 TCGA-GR-A4D4 
        2.04        31.73         4.57       106.09        26.70 

$`AMP PEAK 6(16P11.2) WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 
       35.54        31.10         4.14        27.35        22.32        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23        19.56       196.60       127.30 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        24.69        29.95        46.29 

  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                         2.04                          4.14 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                       106.09                        211.23 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                        26.70                         38.35 
[1] "2.0 - 106.1 (26.7)" "4.1 - 211.2 (38.3)"
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "AMP PEAK 6(16P11.2) MUTATED" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "AMP PEAK 6(16P11.2) MUTATED" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "AMP PEAK 6(16P11.2) MUTATED" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"AMP PEAK 6(16P11.2) WILD-TYPE"   "AMP PEAK 6(16P11.2) MUTATED" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"AMP PEAK 6(16P11.2) WILD-TYPE" "AMP PEAK 6(16P11.2) WILD-TYPE" 
                   TCGA-GR-A4D9 
"AMP PEAK 6(16P11.2) WILD-TYPE" 
[1] "hr=" "2.4"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK 6(16P11.2) MUTATED    3  2
  AMP PEAK 6(16P11.2) WILD-TYPE 10  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(16P11.2) MUTATED      3    2
  AMP PEAK 6(16P11.2) WILD-TYPE   10    6
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  FEMALE                           3                            10
  MALE                             2                             6

Clustering(7) Variable = AMP PEAK 7(XQ27.3) MUTATION ANALYSIS
D7V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 7(XQ27.3) MUTATED    4  0
  AMP PEAK 7(XQ27.3) WILD-TYPE 13  4
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           4                           17 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           0                            4 
$`AMP PEAK 7(XQ27.3) MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        2.04        35.54        31.10        31.73 

$`AMP PEAK 7(XQ27.3) WILD-TYPE`
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        26.70        24.69        29.95        46.29 

  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                        2.04                         4.14 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                       35.54                       211.23 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                      31.415                       41.160 
[1] "2.0 - 35.5 (31.4)"  "4.1 - 211.2 (41.2)"
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D9 
"AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D9 
"AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-FA-A4XK                   TCGA-FF-8041 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8042                   TCGA-FF-8043 
  "AMP PEAK 7(XQ27.3) MUTATED"   "AMP PEAK 7(XQ27.3) MUTATED" 
                  TCGA-FF-8047                   TCGA-FF-8061 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-FF-8062                   TCGA-FM-8000 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6324                   TCGA-G8-6325 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6326                   TCGA-G8-6906 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6907                   TCGA-G8-6909 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-G8-6914                   TCGA-GR-7351 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-7353                   TCGA-GR-A4D4 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D5                   TCGA-GR-A4D6 
"AMP PEAK 7(XQ27.3) WILD-TYPE" "AMP PEAK 7(XQ27.3) WILD-TYPE" 
                  TCGA-GR-A4D9 
"AMP PEAK 7(XQ27.3) WILD-TYPE" 
[1] "hr="     "8.8e+07"
D7V2, continuous
D7V3, binary
                              cls
clus                            0  1
  AMP PEAK 7(XQ27.3) MUTATED    3  1
  AMP PEAK 7(XQ27.3) WILD-TYPE 10  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 7(XQ27.3) MUTATED      3    1
  AMP PEAK 7(XQ27.3) WILD-TYPE   10    7
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  FEMALE                          3                           10
  MALE                            1                            7

Clustering(8) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.1) MUTATED    3  1
  DEL PEAK  2(1P13.1) WILD-TYPE 14  3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            4                            17 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-G8-6325 TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D6 
       51.98       106.09        74.10        29.95 

$`DEL PEAK  2(1P13.1) 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-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       22.32         4.57        41.16        47.38       211.23        19.56 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      196.60       127.30        26.70        24.69        46.29 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                        29.95                          2.04 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       106.09                        211.23 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                        63.04                         31.10 
[1] "29.9 - 106.1 (63.0)" "2.0 - 211.2 (31.1)" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "DEL PEAK  2(1P13.1) MUTATED" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-GR-A4D9 
"DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "DEL PEAK  2(1P13.1) MUTATED" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-GR-A4D9 
"DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  2(1P13.1) WILD-TYPE" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
  "DEL PEAK  2(1P13.1) MUTATED" "DEL PEAK  2(1P13.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  2(1P13.1) WILD-TYPE"   "DEL PEAK  2(1P13.1) MUTATED" 
                   TCGA-GR-A4D9 
"DEL PEAK  2(1P13.1) WILD-TYPE" 
[1] "hr=" "1.4"
D8V2, continuous
D8V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    1  3
  DEL PEAK  2(1P13.1) WILD-TYPE 12  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1    3
  DEL PEAK  2(1P13.1) WILD-TYPE   12    5
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                           1                            12
  MALE                             3                             5

Clustering(9) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q43) MUTATED    4  0
  DEL PEAK  3(1Q43) WILD-TYPE 13  4
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          4                          17 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          0                           4 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D9 
       31.10        31.73         4.14        46.29 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
        2.04        35.54        27.35        22.32         4.57        41.16 
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       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      127.30        74.10        26.70        24.69        29.95 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       4.14                        2.04 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      46.29                      211.23 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     31.415                      35.540 
[1] "4.1 - 46.3 (31.4)"  "2.0 - 211.2 (35.5)"
                 TCGA-FA-A4XK                  TCGA-FF-8041 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
  "DEL PEAK  3(1Q43) MUTATED"   "DEL PEAK  3(1Q43) MUTATED" 
                 TCGA-FF-8047                  TCGA-FF-8061 
  "DEL PEAK  3(1Q43) MUTATED" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8062                  TCGA-FM-8000 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6324                  TCGA-G8-6325 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6326                  TCGA-G8-6906 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6907                  TCGA-G8-6909 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6914                  TCGA-GR-7351 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-7353                  TCGA-GR-A4D4 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D9 
  "DEL PEAK  3(1Q43) MUTATED" 
                 TCGA-FA-A4XK                  TCGA-FF-8041 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
  "DEL PEAK  3(1Q43) MUTATED"   "DEL PEAK  3(1Q43) MUTATED" 
                 TCGA-FF-8047                  TCGA-FF-8061 
  "DEL PEAK  3(1Q43) MUTATED" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8062                  TCGA-FM-8000 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6324                  TCGA-G8-6325 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6326                  TCGA-G8-6906 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6907                  TCGA-G8-6909 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6914                  TCGA-GR-7351 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-7353                  TCGA-GR-A4D4 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D9 
  "DEL PEAK  3(1Q43) MUTATED" 
                 TCGA-FA-A4XK                  TCGA-FF-8041 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
  "DEL PEAK  3(1Q43) MUTATED"   "DEL PEAK  3(1Q43) MUTATED" 
                 TCGA-FF-8047                  TCGA-FF-8061 
  "DEL PEAK  3(1Q43) MUTATED" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-FF-8062                  TCGA-FM-8000 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6324                  TCGA-G8-6325 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6326                  TCGA-G8-6906 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6907                  TCGA-G8-6909 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G8-6914                  TCGA-GR-7351 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-7353                  TCGA-GR-A4D4 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-GR-A4D9 
  "DEL PEAK  3(1Q43) MUTATED" 
[1] "hr="     "2.3e+08"
D9V2, continuous
D9V3, binary
                             cls
clus                          0 1
  DEL PEAK  3(1Q43) MUTATED   4 0
  DEL PEAK  3(1Q43) WILD-TYPE 9 8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      4    0
  DEL PEAK  3(1Q43) WILD-TYPE    9    8
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                         4                           9
  MALE                           0                           8

Clustering(10) Variable = DEL PEAK  4(2Q23.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q23.1) MUTATED    3  1
  DEL PEAK  4(2Q23.1) WILD-TYPE 14  3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            4                            17 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  4(2Q23.1) MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-7351 
       31.73         4.14        41.16       127.30 

$`DEL PEAK  4(2Q23.1) 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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       106.09       196.60 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        26.70        24.69        29.95        46.29 

  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                         4.14                          2.04 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                       127.30                        211.23 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                       36.445                        31.100 
[1] "4.1 - 127.3 (36.4)" "2.0 - 211.2 (31.1)"
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
"DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
"DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
  "DEL PEAK  4(2Q23.1) MUTATED" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  4(2Q23.1) WILD-TYPE"   "DEL PEAK  4(2Q23.1) MUTATED" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK  4(2Q23.1) WILD-TYPE" "DEL PEAK  4(2Q23.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
"DEL PEAK  4(2Q23.1) WILD-TYPE" 
[1] "hr=" "1.9"
D10V2, continuous
D10V3, binary
                               cls
clus                            0 1
  DEL PEAK  4(2Q23.1) MUTATED   4 0
  DEL PEAK  4(2Q23.1) WILD-TYPE 9 8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      4    0
  DEL PEAK  4(2Q23.1) WILD-TYPE    9    8
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  FEMALE                           4                             9
  MALE                             0                             8

Clustering(11) Variable = DEL PEAK  5(6Q14.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(6Q14.1) MUTATED    5  1
  DEL PEAK  5(6Q14.1) WILD-TYPE 12  3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            6                            15 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  5(6Q14.1) MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D5 TCGA-GR-A4D9 
        2.04        31.10        51.98       211.23        24.69        46.29 

$`DEL PEAK  5(6Q14.1) WILD-TYPE`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       35.54        31.73         4.14        27.35        22.32         4.57 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       41.16        47.38        19.56       106.09       196.60       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       74.10        26.70        29.95 

  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                         2.04                          4.14 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                       38.695                        31.730 
[1] "2.0 - 211.2 (38.7)" "4.1 - 196.6 (31.7)"
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  5(6Q14.1) MUTATED" 
[1] "hr="     "8.5e+08"
D11V2, continuous
D11V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(6Q14.1) MUTATED    3  3
  DEL PEAK  5(6Q14.1) WILD-TYPE 10  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      3    3
  DEL PEAK  5(6Q14.1) WILD-TYPE   10    5
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  FEMALE                           3                            10
  MALE                             3                             5

Clustering(12) Variable = DEL PEAK  6(6Q23.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(6Q23.3) MUTATED    3  2
  DEL PEAK  6(6Q23.3) WILD-TYPE 14  2
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            16 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            2                             2 
$`DEL PEAK  6(6Q23.3) MUTATED`
TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D9 
       51.98       211.23       106.09        24.69        46.29 

$`DEL PEAK  6(6Q23.3) 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-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6914 
       22.32         4.57        41.16        47.38        19.56       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      127.30        74.10        26.70        29.95 

  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                        24.69                          2.04 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                       51.980                        30.525 
[1] "24.7 - 211.2 (52.0)" "2.0 - 196.6 (30.5)" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  6(6Q23.3) MUTATED" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  6(6Q23.3) MUTATED" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK  6(6Q23.3) WILD-TYPE"   "DEL PEAK  6(6Q23.3) MUTATED" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK  6(6Q23.3) WILD-TYPE" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
  "DEL PEAK  6(6Q23.3) MUTATED" "DEL PEAK  6(6Q23.3) WILD-TYPE" 
                   TCGA-GR-A4D9 
  "DEL PEAK  6(6Q23.3) MUTATED" 
[1] "hr=" "1.4"
D12V2, continuous
D12V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(6Q23.3) MUTATED    2  3
  DEL PEAK  6(6Q23.3) WILD-TYPE 11  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(6Q23.3) MUTATED      2    3
  DEL PEAK  6(6Q23.3) WILD-TYPE   11    5
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  FEMALE                           2                            11
  MALE                             3                             5

Clustering(13) Variable = DEL PEAK 10(9P21.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(9P21.3) MUTATED    6  1
  DEL PEAK 10(9P21.3) WILD-TYPE 11  3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            14 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            1                             3 
$`DEL PEAK 10(9P21.3) MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8047 TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D6 
        2.04        31.10         4.14        51.98       211.23        29.95 
TCGA-GR-A4D9 
       46.29 

$`DEL PEAK 10(9P21.3) 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        41.16 
TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       47.38        19.56       106.09       196.60       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 
       26.70        24.69 

  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                         2.04                          4.57 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                       31.100                        33.635 
[1] "2.0 - 211.2 (31.1)" "4.6 - 196.6 (33.6)"
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-GR-A4D9 
  "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-GR-A4D9 
  "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-FA-A4XK                    TCGA-FF-8041 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8042                    TCGA-FF-8043 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
  "DEL PEAK 10(9P21.3) MUTATED" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-G8-6907                    TCGA-G8-6909 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-G8-6914                    TCGA-GR-7351 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-7353                    TCGA-GR-A4D4 
"DEL PEAK 10(9P21.3) WILD-TYPE" "DEL PEAK 10(9P21.3) WILD-TYPE" 
                   TCGA-GR-A4D5                    TCGA-GR-A4D6 
"DEL PEAK 10(9P21.3) WILD-TYPE"   "DEL PEAK 10(9P21.3) MUTATED" 
                   TCGA-GR-A4D9 
  "DEL PEAK 10(9P21.3) MUTATED" 
[1] "hr="     "8.5e+08"
D13V2, continuous
D13V3, binary
                               cls
clus                            0 1
  DEL PEAK 10(9P21.3) MUTATED   4 3
  DEL PEAK 10(9P21.3) WILD-TYPE 9 5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      4    3
  DEL PEAK 10(9P21.3) WILD-TYPE    9    5
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  FEMALE                           4                             9
  MALE                             3                             5

Clustering(14) Variable = DEL PEAK 11(10Q23.31) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 11(10Q23.31) MUTATED    3  1
  DEL PEAK 11(10Q23.31) WILD-TYPE 14  3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              17 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              1                               3 
$`DEL PEAK 11(10Q23.31) MUTATED`
TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       19.56        74.10        26.70        29.95 

$`DEL PEAK 11(10Q23.31) 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-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       22.32         4.57        41.16        51.98        47.38       211.23 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
      106.09       196.60       127.30        24.69        46.29 

  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                          19.56                            2.04 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                          74.10                          211.23 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                         28.325                          35.540 
[1] "19.6 - 74.1 (28.3)" "2.0 - 211.2 (35.5)"
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D9 
"DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D9 
"DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GR-A4D9 
"DEL PEAK 11(10Q23.31) WILD-TYPE" 
[1] "hr=" "5.3"
D14V2, continuous
D14V3, binary
                                 cls
clus                               0  1
  DEL PEAK 11(10Q23.31) MUTATED    3  1
  DEL PEAK 11(10Q23.31) WILD-TYPE 10  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      3    1
  DEL PEAK 11(10Q23.31) WILD-TYPE   10    7
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  FEMALE                             3                              10
  MALE                               1                               7

Clustering(15) Variable = DEL PEAK 12(13Q14.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(13Q14.2) MUTATED    2  1
  DEL PEAK 12(13Q14.2) WILD-TYPE 15  3
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             18 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             1                              3 
$`DEL PEAK 12(13Q14.2) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-A4D4 
       31.73        19.56        26.70 

$`DEL PEAK 12(13Q14.2) 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-G8-6909 
        4.57        41.16        51.98        47.38       211.23       106.09 
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 

  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                         19.56                           2.04 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                         31.73                         211.23 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                         26.70                          38.35 
[1] "19.6 - 31.7 (26.7)" "2.0 - 211.2 (38.3)"
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 12(13Q14.2) MUTATED" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 12(13Q14.2) MUTATED" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 12(13Q14.2) MUTATED" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 12(13Q14.2) WILD-TYPE"   "DEL PEAK 12(13Q14.2) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 12(13Q14.2) WILD-TYPE" "DEL PEAK 12(13Q14.2) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 12(13Q14.2) WILD-TYPE" 
[1] "hr="     "3.7e+09"
D15V2, continuous
D15V3, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q14.2) MUTATED    3  0
  DEL PEAK 12(13Q14.2) WILD-TYPE 10  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q14.2) MUTATED      3    0
  DEL PEAK 12(13Q14.2) WILD-TYPE   10    8
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  FEMALE                            3                             10
  MALE                              0                              8

Clustering(16) Variable = DEL PEAK 13(13Q33.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(13Q33.3) MUTATED    4  0
  DEL PEAK 13(13Q33.3) WILD-TYPE 13  4
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             17 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             0                              4 
$`DEL PEAK 13(13Q33.3) MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-A4D4 
       31.10        31.73       127.30        26.70 

$`DEL PEAK 13(13Q33.3) 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 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60        74.10        24.69        29.95        46.29 

  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                         26.70                           2.04 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                        31.415                         35.540 
[1] "26.7 - 127.3 (31.4)" "2.0 - 211.2 (35.5)" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
  "DEL PEAK 13(13Q33.3) MUTATED"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
  "DEL PEAK 13(13Q33.3) MUTATED"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
  "DEL PEAK 13(13Q33.3) MUTATED"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 13(13Q33.3) WILD-TYPE"   "DEL PEAK 13(13Q33.3) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 13(13Q33.3) WILD-TYPE" "DEL PEAK 13(13Q33.3) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 13(13Q33.3) WILD-TYPE" 
[1] "hr="     "2.6e+08"
D16V2, continuous
D16V3, binary
                                cls
clus                             0 1
  DEL PEAK 13(13Q33.3) MUTATED   4 0
  DEL PEAK 13(13Q33.3) WILD-TYPE 9 8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(13Q33.3) MUTATED      4    0
  DEL PEAK 13(13Q33.3) WILD-TYPE    9    8
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  FEMALE                            4                              9
  MALE                              0                              8

Clustering(17) Variable = DEL PEAK 14(15Q15.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(15Q15.1) MUTATED    5  1
  DEL PEAK 14(15Q15.1) WILD-TYPE 12  3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 14(15Q15.1) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       31.73        19.56       127.30        74.10        26.70        29.95 

$`DEL PEAK 14(15Q15.1) 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-G8-6909 
        4.57        41.16        51.98        47.38       211.23       106.09 
TCGA-G8-6914 TCGA-GR-A4D5 TCGA-GR-A4D9 
      196.60        24.69        46.29 

  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                         19.56                           2.04 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                         30.84                          35.54 
[1] "19.6 - 127.3 (30.8)" "2.0 - 211.2 (35.5)" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 14(15Q15.1) WILD-TYPE" 
[1] "hr=" "1.4"
D17V2, continuous
D17V3, binary
                                cls
clus                             0 1
  DEL PEAK 14(15Q15.1) MUTATED   5 1
  DEL PEAK 14(15Q15.1) WILD-TYPE 8 7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      5    1
  DEL PEAK 14(15Q15.1) WILD-TYPE    8    7
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  FEMALE                            5                              8
  MALE                              1                              7

Clustering(18) Variable = DEL PEAK 15(15Q21.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(15Q21.1) MUTATED    5  1
  DEL PEAK 15(15Q21.1) WILD-TYPE 12  3
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 15(15Q21.1) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       31.73        19.56       127.30        74.10        26.70        29.95 

$`DEL PEAK 15(15Q21.1) 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-G8-6909 
        4.57        41.16        51.98        47.38       211.23       106.09 
TCGA-G8-6914 TCGA-GR-A4D5 TCGA-GR-A4D9 
      196.60        24.69        46.29 

  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                         19.56                           2.04 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                         30.84                          35.54 
[1] "19.6 - 127.3 (30.8)" "2.0 - 211.2 (35.5)" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 15(15Q21.1) MUTATED" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 15(15Q21.1) MUTATED"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 15(15Q21.1) MUTATED" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 15(15Q21.1) MUTATED"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 15(15Q21.1) WILD-TYPE" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 15(15Q21.1) MUTATED" "DEL PEAK 15(15Q21.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
  "DEL PEAK 15(15Q21.1) MUTATED"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 15(15Q21.1) WILD-TYPE"   "DEL PEAK 15(15Q21.1) MUTATED" 
                    TCGA-GR-A4D9 
"DEL PEAK 15(15Q21.1) WILD-TYPE" 
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
                                cls
clus                             0 1
  DEL PEAK 15(15Q21.1) MUTATED   5 1
  DEL PEAK 15(15Q21.1) WILD-TYPE 8 7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q21.1) MUTATED      5    1
  DEL PEAK 15(15Q21.1) WILD-TYPE    8    7
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  FEMALE                            5                              8
  MALE                              1                              7

Clustering(19) Variable = DEL PEAK 16(16P13.13) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(16P13.13) MUTATED    3  0
  DEL PEAK 16(16P13.13) WILD-TYPE 14  4
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              3                              18 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              0                               4 
$`DEL PEAK 16(16P13.13) MUTATED`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FM-8000 
       35.54        31.73         4.57 

$`DEL PEAK 16(16P13.13) WILD-TYPE`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 
        2.04        31.10         4.14        27.35        22.32        41.16 
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       106.09       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 

  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                           4.57                            2.04 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                          35.54                          211.23 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                          31.73                           36.13 
[1] "4.6 - 35.5 (31.7)"  "2.0 - 211.2 (36.1)"
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D9 
"DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D9 
"DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-FA-A4XK                      TCGA-FF-8041 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8042                      TCGA-FF-8043 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-FF-8047                      TCGA-FF-8061 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-FF-8062                      TCGA-FM-8000 
"DEL PEAK 16(16P13.13) WILD-TYPE"   "DEL PEAK 16(16P13.13) MUTATED" 
                     TCGA-G8-6324                      TCGA-G8-6325 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6326                      TCGA-G8-6906 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6907                      TCGA-G8-6909 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-G8-6914                      TCGA-GR-7351 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-7353                      TCGA-GR-A4D4 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D5                      TCGA-GR-A4D6 
"DEL PEAK 16(16P13.13) WILD-TYPE" "DEL PEAK 16(16P13.13) WILD-TYPE" 
                     TCGA-GR-A4D9 
"DEL PEAK 16(16P13.13) WILD-TYPE" 
[1] "hr="     "7.9e+07"
D19V2, continuous
D19V3, binary
                                 cls
clus                               0  1
  DEL PEAK 16(16P13.13) MUTATED    3  0
  DEL PEAK 16(16P13.13) WILD-TYPE 10  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(16P13.13) MUTATED      3    0
  DEL PEAK 16(16P13.13) WILD-TYPE   10    8
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  FEMALE                             3                              10
  MALE                               0                               8

Clustering(20) Variable = DEL PEAK 17(16Q23.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(16Q23.1) MUTATED    3  0
  DEL PEAK 17(16Q23.1) WILD-TYPE 14  4
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             3                             18 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             0                              4 
$`DEL PEAK 17(16Q23.1) MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
       31.73         4.14        26.70 

$`DEL PEAK 17(16Q23.1) 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 
       41.16        51.98        47.38       211.23        19.56       106.09 
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 

  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                          4.14                           2.04 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         31.73                         211.23 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         26.70                          38.35 
[1] "4.1 - 31.7 (26.7)"  "2.0 - 211.2 (38.3)"
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
  "DEL PEAK 17(16Q23.1) MUTATED" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
  "DEL PEAK 17(16Q23.1) MUTATED" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-FF-8047                     TCGA-FF-8061 
  "DEL PEAK 17(16Q23.1) MUTATED" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 17(16Q23.1) WILD-TYPE"   "DEL PEAK 17(16Q23.1) MUTATED" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 17(16Q23.1) WILD-TYPE" "DEL PEAK 17(16Q23.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 17(16Q23.1) WILD-TYPE" 
[1] "hr="     "7.9e+07"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    3  0
  DEL PEAK 17(16Q23.1) WILD-TYPE 10  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      3    0
  DEL PEAK 17(16Q23.1) WILD-TYPE   10    8
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  FEMALE                            3                             10
  MALE                              0                              8

Clustering(21) Variable = DEL PEAK 18(17Q24.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  1
  DEL PEAK 18(17Q24.1) WILD-TYPE 15  3
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             3                             18 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 18(17Q24.1) MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6907 
        2.04         4.57        19.56 

$`DEL PEAK 18(17Q24.1) 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-G8-6909 TCGA-G8-6914 
       41.16        51.98        47.38       211.23       106.09       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 

  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                          2.04                           4.14 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                         19.56                         211.23 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                          4.57                          38.35 
[1] "2.0 - 19.6 (4.6)"   "4.1 - 211.2 (38.3)"
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 18(17Q24.1) WILD-TYPE"   "DEL PEAK 18(17Q24.1) MUTATED" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 18(17Q24.1) WILD-TYPE"   "DEL PEAK 18(17Q24.1) MUTATED" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FF-8041 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 18(17Q24.1) WILD-TYPE"   "DEL PEAK 18(17Q24.1) MUTATED" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
  "DEL PEAK 18(17Q24.1) MUTATED" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 18(17Q24.1) WILD-TYPE" "DEL PEAK 18(17Q24.1) WILD-TYPE" 
                    TCGA-GR-A4D9 
"DEL PEAK 18(17Q24.1) WILD-TYPE" 
[1] "hr="     "9.7e+09"
D21V2, continuous
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  1
  DEL PEAK 18(17Q24.1) WILD-TYPE 11  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17Q24.1) MUTATED      2    1
  DEL PEAK 18(17Q24.1) WILD-TYPE   11    7
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  FEMALE                            2                             11
  MALE                              1                              7
> q(save="no")
